Linter fixes for poretools

tools/poretools/.lint_skip

@@ -1,7 +1 @@
-InputsNameDuplicate
-InputsNameRedundantArgument
-InputsSelectOptionDuplicateText
-InputsSelectOptionDuplicateValue
-TestsParamInInputs
 ToolVersionPEP404
-XMLOrder

tools/poretools/macros.xml

@@ -12,6 +12,7 @@
         </xrefs>
     </xml>
     <token name="@VERSION@">0.6.1a1</token>
+    <token name="@PROFILE@">23.1</token>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1093/bioinformatics/btu555</citation>
@@ -24,7 +25,7 @@
             <option value="svg">SVG</option>
             <yield />
         </param>
-        <param name="theme_bw" argument="--theme-bw" type="boolean" truevalue="--theme-bw" falsevalue="" label="Use a monochrome color scheme" />
+        <param argument="--theme-bw" type="boolean" truevalue="--theme-bw" falsevalue="" label="Use a monochrome color scheme" />
     </xml>
     <xml name="image_output">
         <data name="output" format="png">
@@ -36,7 +37,7 @@
         </data>
     </xml>
     <xml name="stat_options">
-        <param name="type" argument="--type" type="select" label="Filter by type of read">
+        <param argument="--type" type="select" label="Filter by type of read">
             <option value="all" selected="true">All</option>
             <option value="fwd">Forward reads</option>
             <option value="rev">Reverse reads</option>
@@ -49,9 +50,8 @@
         <param name="input" ftype="fast5.tar" value="poretools-in1.tar.bz2" />
     </xml>
     <xml name="length_options">
-        <param name="min_length" argument="--min-length" type="integer" value="0" label="Minimum read length" />
-        <param name="max_length" argument="--max-length" type="integer" value="1000000000" label="Maximum read length" />
+        <param argument="--min-length" type="integer" value="0" label="Minimum read length" />
+        <param argument="--max-length" type="integer" value="1000000000" label="Maximum read length" />
     </xml>
     <token name="@MPLBACKEND@"><![CDATA[export MPLBACKEND="agg" &&]]></token>
-    <token name="@profile@">18.09</token>
 </macros>

tools/poretools/poretools_events.xml

@@ -1,10 +1,9 @@
-<?xml version="1.0"?>
-<tool id="poretools_events" name="Extract nanopore events" version="@[email protected]">
+<tool id="poretools_events" name="Extract nanopore events" version="@[email protected]" profile="@PROFILE@">
     <description>from a set of sequencing reads</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command detect_errors="aggressive">
     <![CDATA[

tools/poretools/poretools_extract.xml

@@ -1,10 +1,9 @@
-<?xml version="1.0"?>
-<tool id="poretools_extract" name="Extract reads" version="@[email protected]">
+<tool id="poretools_extract" name="Extract reads" version="@[email protected]" profile="@PROFILE@">
     <description>in FASTA or FASTQ format from nanopore files</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command detect_errors="aggressive">
     <![CDATA[

tools/poretools/poretools_hist.xml

@@ -1,10 +1,9 @@
-<?xml version="1.0"?>
-<tool id="poretools_hist" name="Generate histogram" version="@[email protected]">
+<tool id="poretools_hist" name="Generate histogram" version="@[email protected]" profile="@PROFILE@">
     <description>of nanopore read lengths</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command detect_errors="aggressive">
     <![CDATA[
@@ -16,7 +15,7 @@ poretools hist '$input' --saveas histogram.$extension --min-length $min_length -
         <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" />
         <expand macro="plot_options" />
         <expand macro="length_options" />
-        <param name="num_bins" argument="--num-bins" type="integer" value="50" label="Number of bins in the histogram" />
+        <param argument="--num-bins" type="integer" value="50" label="Number of bins in the histogram" />
     </inputs>
     <outputs>
         <expand macro="image_output" />

tools/poretools/poretools_nucdist.xml

@@ -1,10 +1,9 @@
-<?xml version="1.0"?>
-<tool id="poretools_nucdist" name="Show nucleotide" version="@[email protected]">
+<tool id="poretools_nucdist" name="Show nucleotide" version="@[email protected]" profile="@PROFILE@">
     <description>distribution in nanopore sequencing reads</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command detect_errors="aggressive">
     <![CDATA[

tools/poretools/poretools_occupancy.xml

@@ -1,10 +1,9 @@
-<?xml version="1.0"?>
-<tool id="poretools_occupancy" name="Plot performance" version="@[email protected]">
+<tool id="poretools_occupancy" name="Plot performance" version="@[email protected]" profile="@PROFILE@">
     <description>per cell in nanopore reads</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command detect_errors="aggressive">
     <![CDATA[
@@ -24,7 +23,7 @@ mv occupancy.$extension '$output'
             <option value="pdf">PDF</option>
             <option value="svg">SVG</option>
         </param>
-        <param name="plot_type" argument="--plot-type" type="select" label="Plot type to generate">
+        <param argument="--plot-type" type="select" label="Plot type to generate">
             <option value="read_count">Read count</option>
             <option value="total_bp">Total base pairs</option>
         </param>

tools/poretools/poretools_qualdist.xml

@@ -1,10 +1,9 @@
-<?xml version="1.0"?>
-<tool id="poretools_qualdist" name="Show quality" version="@[email protected]">
+<tool id="poretools_qualdist" name="Show quality" version="@[email protected]" profile="@PROFILE@">
     <description>score distribution in nanopore sequencing reads</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command detect_errors="aggressive">
     <![CDATA[

tools/poretools/poretools_qualpos.xml

@@ -1,10 +1,9 @@
-<?xml version="1.0"?>
-<tool id="poretools_qualpos" name="Generate box-whisker" version="@[email protected]">
+<tool id="poretools_qualpos" name="Generate box-whisker" version="@[email protected]" profile="@PROFILE@">
     <description>plot of quality score distribution over positions in nanopore reads</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command detect_errors="aggressive">
     <![CDATA[
@@ -14,13 +13,9 @@ poretools qualpos '$input' --saveas qualpos.$extension --min-length $min_length
     </command>
     <inputs>
         <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" />
-        <expand macro="plot_options">
-            <option value="pdf">PDF</option>
-            <option value="svg">SVG</option>
-        </expand>
-        <param name="theme_bw" argument="--theme-bw" type="boolean" truevalue="--theme-bw" falsevalue="" label="Use a monochrome color " />
+        <expand macro="plot_options"/>
         <expand macro="length_options" />
-        <param name="bin_width" argument="--bin-width" type="integer" value="1000" label="The width of bins" />
+        <param argument="--bin-width" type="integer" value="1000" label="The width of bins" />
     </inputs>
     <outputs>
         <expand macro="image_output">

tools/poretools/poretools_squiggle.xml

@@ -1,10 +1,9 @@
-<?xml version="1.0"?>
-<tool id="poretools_squiggle" name="Plot signals" version="@[email protected]" profile="@profile@">
+<tool id="poretools_squiggle" name="Plot signals" version="@[email protected]" profile="@PROFILE@">
     <description>for nanopore reads</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command detect_errors="aggressive">
     <![CDATA[
@@ -15,7 +14,7 @@ poretools squiggle '$input' --saveas $extension --num-facets $num_facets $theme_
     <inputs>
         <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" />
         <expand macro="plot_options" />
-        <param name="num_facets" argument="--num-facets" type="integer" value="6" label="Number of plot facets" />
+        <param argument="--num-facets" type="integer" value="6" label="Number of plot facets" />
     </inputs>
     <outputs>
         <data format="txt" name="output">

tools/poretools/poretools_stats.xml

@@ -1,10 +1,9 @@
-<?xml version="1.0"?>
-<tool id="poretools_stats" name="Read length statistics" version="@[email protected]">
+<tool id="poretools_stats" name="Read length statistics" version="@[email protected]" profile="@PROFILE@">
     <description>from a set of FAST5 files</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command detect_errors="aggressive">
     <![CDATA[

tools/poretools/poretools_tabular.xml

@@ -1,10 +1,9 @@
-<?xml version="1.0"?>
-<tool id="poretools_tabular" name="Extract FASTQ" version="@[email protected]">
+<tool id="poretools_tabular" name="Extract FASTQ" version="@[email protected]" profile="@PROFILE@">
     <description>in tabular format from a set of FAST5 files</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command detect_errors="aggressive">
     <![CDATA[
@@ -21,32 +20,27 @@
     <tests>
         <test>
             <expand macro="test_input" />
-            <param name="types" value="fwd" />
-            <param name="detailed" value="true" />
+            <param name="type" value="fwd" />
             <output name="output" file="poretools-tabular-out1.tabular" ftype="tabular" />
         </test>
         <test>
             <expand macro="test_input" />
-            <param name="types" value="rev" />
-            <param name="detailed" value="false" />
+            <param name="type" value="rev" />
             <output name="output" file="poretools-tabular-out2.tabular" ftype="tabular" />
         </test>
         <test>
             <expand macro="test_input" />
-            <param name="types" value="2D" />
-            <param name="detailed" value="true" />
+            <param name="type" value="2D" />
             <output name="output" file="poretools-tabular-out3.tabular" ftype="tabular" />
         </test>
         <test>
             <expand macro="test_input" />
-            <param name="types" value="best" />
-            <param name="detailed" value="false" />
+            <param name="type" value="best" />
             <output name="output" file="poretools-tabular-out4.tabular" ftype="tabular" />
         </test>
         <test>
             <expand macro="test_input" />
-            <param name="types" value="all" />
-            <param name="detailed" value="true" />
+            <param name="type" value="all" />
             <output name="output" file="poretools-tabular-out5.tabular" ftype="tabular" />
         </test>
     </tests>

tools/poretools/poretools_times.xml

@@ -1,10 +1,9 @@
-<?xml version="1.0"?>
-<tool id="poretools_times" name="Extract time" version="@[email protected]">
+<tool id="poretools_times" name="Extract time" version="@[email protected]" profile="@PROFILE@">
     <description>and channel information from a set of FAST5 files</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command detect_errors="aggressive">
     <![CDATA[
@@ -20,34 +19,8 @@
     <tests>
         <test>
             <expand macro="test_input" />
-            <param name="types" value="fwd" />
-            <param name="detailed" value="true" />
             <output name="output" file="poretools-times-out1.tabular" ftype="tabular" />
         </test>
-        <test>
-            <expand macro="test_input" />
-            <param name="types" value="rev" />
-            <param name="detailed" value="false" />
-            <output name="output" file="poretools-times-out2.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <expand macro="test_input" />
-            <param name="types" value="2D" />
-            <param name="detailed" value="true" />
-            <output name="output" file="poretools-times-out3.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <expand macro="test_input" />
-            <param name="types" value="best" />
-            <param name="detailed" value="false" />
-            <output name="output" file="poretools-times-out4.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <expand macro="test_input" />
-            <param name="types" value="all" />
-            <param name="detailed" value="true" />
-            <output name="output" file="poretools-times-out5.tabular" ftype="tabular" />
-        </test>
     </tests>
     <help>
         Collect read size statistics from a set of FAST5 files.

tools/poretools/poretools_winner.xml

@@ -1,10 +1,9 @@
-<?xml version="1.0"?>
-<tool id="poretools_winner" name="Get longest read" version="@[email protected]">
+<tool id="poretools_winner" name="Get longest read" version="@[email protected]" profile="@PROFILE@">
     <description>from a set of FAST5 files.</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command detect_errors="aggressive">
     <![CDATA[
@@ -21,22 +20,22 @@
     <tests>
         <test>
             <expand macro="test_input" />
-            <param name="types" value="fwd" />
+            <param name="type" value="fwd" />
             <output name="output" file="poretools-winner-out1.tabular" ftype="tabular" />
         </test>
         <test>
             <expand macro="test_input" />
-            <param name="types" value="rev" />
+            <param name="type" value="rev" />
             <output name="output" file="poretools-winner-out2.tabular" ftype="tabular" />
         </test>
         <test>
             <expand macro="test_input" />
-            <param name="types" value="2D" />
+            <param name="type" value="2D" />
             <output name="output" file="poretools-winner-out3.tabular" ftype="tabular" />
         </test>
         <test>
             <expand macro="test_input" />
-            <param name="types" value="best" />
+            <param name="type" value="best" />
             <output name="output" file="poretools-winner-out4.tabular" ftype="tabular" />
         </test>
     </tests>

tools/poretools/poretools_yield_plot.xml

@@ -1,10 +1,9 @@
-<?xml version="1.0"?>
-<tool id="poretools_yield_plot" name="Collector’s curve" version="@[email protected]">
+<tool id="poretools_yield_plot" name="Collector’s curve" version="@[email protected]" profile="@PROFILE@">
     <description>of sequencing yield over time</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <command detect_errors="aggressive">
     <![CDATA[
@@ -19,7 +18,7 @@ poretools yield_plot '$input' --saveas plot.$extension --plot-type $plot_type
     </command>
     <inputs>
         <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" />
-        <param name="plot_type" argument="--plot-type" type="select" label="Plot reads or base pairs">
+        <param argument="--plot-type" type="select" label="Plot reads or base pairs">
             <option value="reads">Reads</option>
             <option value="basepairs">Base pairs</option>
         </param>