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Updating tools/polypolish from version 0.5.0 to 0.6.0 #5749

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Nov 12, 2024
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Updating tools/polypolish from version 0.5.0 to 0.6.0 #5749

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81e0e20
Updating tools/polypolish from version 0.5.0 to 0.6.0
Feb 5, 2024
b544367
reformat
bgruening May 18, 2024
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79 changes: 37 additions & 42 deletions tools/polypolish/macro.xml
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Original file line number Diff line number Diff line change
@@ -1,48 +1,43 @@

<macros>
<token name="@TOOL_VERSION@">0.5.0</token>
<token name="@VERSION_SUFFIX@">2</token>
<token name="@PROFILE@">21.05</token>

<token name="@THREADS@"><![CDATA[
<token name="@TOOL_VERSION@">0.6.0</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@PROFILE@">21.05</token>
<token name="@THREADS@"><![CDATA[
##compute the number of ADDITIONAL threads to be used by samtools (-@)
addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
]]></token>

<xml name="version_command">
<version_command><![CDATA[polypolish -V]]></version_command>
</xml>
<xml name="xrefs">
<xrefs>
<xref type='bio.tools'>Polypolish</xref>
</xrefs>
</xml>
<xml name="requirements">
<requirements>
<requirement type="package" version="@TOOL_VERSION@">polypolish</requirement>
<requirement type="package" version="1.19">samtools</requirement>
</requirements>
</xml>
<xml name="citations">
<citations>
<citation type="doi">10.1371/journal.pcbi.1009802</citation>
</citations>
</xml>
<!-- Filter option of polypolish -->
<xml name="filter_option">
<conditional name="insert_filter">
<param name="filter_select" type="select" label="Filter by insert size ? [recommanded]"
help="Exclude some alignments based on their insert size. It reduce the number of excessive alignments,
particularly near the edges of repeat sequences">
<option value="filter" selected="true">Filter by insert size</option>
<option value="non_filter"> No filtering step</option>
</param>
<when value="filter">
<param argument="--low" type="float" min="0" value="0.1" label="Low percentile threshold" help="Select the lower value to remove [default: 0.1]"/>
<param argument="--high" type="float" min="0" value="99.9" label="High percentile threshold" help="Select the lower value to remove [default: 99.9]"/>
<xml name="version_command">
<version_command><![CDATA[polypolish -V]]></version_command>
</xml>
<xml name="xrefs">
<xrefs>
<xref type="bio.tools">Polypolish</xref>
</xrefs>
</xml>
<xml name="requirements">
<requirements>
<requirement type="package" version="@TOOL_VERSION@">polypolish</requirement>
<requirement type="package" version="1.19.2">samtools</requirement>
</requirements>
</xml>
<xml name="citations">
<citations>
<citation type="doi">10.1371/journal.pcbi.1009802</citation>
</citations>
</xml>
<!-- Filter option of polypolish -->
<xml name="filter_option">
<conditional name="insert_filter">
<param name="filter_select" type="select" label="Filter by insert size ? [recommanded]" help="Exclude some alignments based on their insert size. It reduce the number of excessive alignments, particularly near the edges of repeat sequences">
<option value="filter" selected="true">Filter by insert size</option>
<option value="non_filter"> No filtering step</option>
</param>
<when value="filter">
<param argument="--low" type="float" min="0" value="0.1" label="Low percentile threshold" help="Select the lower value to remove [default: 0.1]"/>
<param argument="--high" type="float" min="0" value="99.9" label="High percentile threshold" help="Select the lower value to remove [default: 99.9]"/>
</when>
<when value="non_filter">
</when>
<when value="non_filter">
</when>
</conditional>
</xml>
</conditional>
</xml>
</macros>
69 changes: 32 additions & 37 deletions tools/polypolish/polypolish.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,9 @@
<macros>
<import>macro.xml</import>
</macros>
<expand macro='xrefs'/>
<expand macro="requirements" />
<expand macro="version_command" />
<expand macro="xrefs"/>
<expand macro="requirements"/>
<expand macro="version_command"/>
<command detect_errors="aggressive"><![CDATA[
ln -s '$input.fasta_file' input_data &&
#*======================================
Expand Down Expand Up @@ -116,8 +116,7 @@
</command>
<inputs>
<section name="input" title="Input sequences" expanded="True">
<param name="fasta_file" type="data" format="fasta" label="Select a draft genome for polishing"
help="Fasta sequence to be cleaned using short-reads data"/>
<param name="fasta_file" type="data" format="fasta" label="Select a draft genome for polishing" help="Fasta sequence to be cleaned using short-reads data"/>
<conditional name="sam_data_type">
<param name="sam_selector" type="select" label="Select aligned data to polish" help="Choose number of aligned sam/bam files. Need aligned file with all possible locations in aligner option">
<option value="single">Single SAM/BAM file</option>
Expand All @@ -143,14 +142,10 @@
</conditional>
</section>
<section name="options" title="Options" expanded="False">
<param argument="--min_depth" type="integer" min="0" value="5" label="Minimal depth"
help="A base must occur at least this many times in the pileup to be considered valid [default: 5]"/>
<param argument="--fraction_invalid" type="float" min="0" value="0.2" max="1" label="Minimal invalid fraction"
help="A base must make up less than this fraction of the read depth to be considered invalid [default: 0.2]"/>
<param argument="--max_errors" type="integer" min="0" value="10" label="Number of mismatch/indels to ignore alignments"
help="Ignore alignments with more than this many mismatches and indels [default: 10]"/>
<param argument="--fraction_valid" type="float" min="0" value="0.5" max="1" label="Minimal valid fraction"
help="A base must make up at least this fraction of the read depth to be considered valid [default: 0.5"/>
<param argument="--min_depth" type="integer" min="0" value="5" label="Minimal depth" help="A base must occur at least this many times in the pileup to be considered valid [default: 5]"/>
<param argument="--fraction_invalid" type="float" min="0" value="0.2" max="1" label="Minimal invalid fraction" help="A base must make up less than this fraction of the read depth to be considered invalid [default: 0.2]"/>
<param argument="--max_errors" type="integer" min="0" value="10" label="Number of mismatch/indels to ignore alignments" help="Ignore alignments with more than this many mismatches and indels [default: 10]"/>
<param argument="--fraction_valid" type="float" min="0" value="0.5" max="1" label="Minimal valid fraction" help="A base must make up at least this fraction of the read depth to be considered valid [default: 0.5"/>
<param name="keep_logfile" type="boolean" truevalue="true" falsevalue="false" label="Keep log file"/>
<param argument="--debug" type="boolean" truevalue="true" falsevalue="false" label="Keep per base information file"/>
</section>
Expand Down Expand Up @@ -369,29 +364,29 @@
<section name="input">
<param name="fasta_file" value="contigs.fa"/>
<conditional name="sam_data_type">
<param name="sam_selector" value="multiple_paired"/>
<param name="paired_collection">
<collection type="list:paired">
<element name="paired_1">
<collection type="paired">
<element name="forward" value="aligned_test_file/alignement_R1.bam" ftype="unsorted.bam"/>
<element name="reverse" value="aligned_test_file/alignement_R2.bam" ftype="unsorted.bam"/>
</collection>
</element>
<element name="paired_2">
<collection type="paired">
<element name="forward" value="aligned_test_file/alignement_R1_bis.bam" ftype="unsorted.bam"/>
<element name="reverse" value="aligned_test_file/alignement_R2_bis.bam" ftype="unsorted.bam"/>
</collection>
</element>
<element name="paired_3">
<collection type="paired">
<element name="forward" value="aligned_test_file/alignement_R1_ter.bam" ftype="unsorted.bam"/>
<element name="reverse" value="aligned_test_file/alignement_R2_ter.bam" ftype="unsorted.bam"/>
</collection>
</element>
</collection>
</param>
<param name="sam_selector" value="multiple_paired"/>
<param name="paired_collection">
<collection type="list:paired">
<element name="paired_1">
<collection type="paired">
<element name="forward" value="aligned_test_file/alignement_R1.bam" ftype="unsorted.bam"/>
<element name="reverse" value="aligned_test_file/alignement_R2.bam" ftype="unsorted.bam"/>
</collection>
</element>
<element name="paired_2">
<collection type="paired">
<element name="forward" value="aligned_test_file/alignement_R1_bis.bam" ftype="unsorted.bam"/>
<element name="reverse" value="aligned_test_file/alignement_R2_bis.bam" ftype="unsorted.bam"/>
</collection>
</element>
<element name="paired_3">
<collection type="paired">
<element name="forward" value="aligned_test_file/alignement_R1_ter.bam" ftype="unsorted.bam"/>
<element name="reverse" value="aligned_test_file/alignement_R2_ter.bam" ftype="unsorted.bam"/>
</collection>
</element>
</collection>
</param>
</conditional>
</section>
<section name="options">
Expand Down Expand Up @@ -429,7 +424,7 @@
<output name="debug_file" value="debug_file_test_2.tsv"/>
</test>
</tests>
<help><![CDATA[
<help><![CDATA[
**What it does**
Polypolish is a tool for polishing genome assemblies with short reads.
Polypolish uses SAM/BAM files where each read has been aligned to all possible locations (not just a single best location).
Expand Down
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