Merge branch 'galaxyproject:main' into pairtools_split

galaxyproject · Apr 5, 2024 · 4ad3ea6 · 4ad3ea6
2 parents e447921 + e9ebcf7
commit 4ad3ea6
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diff --git a/tools/baredsc/macros.xml b/tools/baredsc/macros.xml
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.1.2</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">1.1.3</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">baredsc</requirement>
-            <requirement type="package" version="1.12">gzip</requirement>
+            <requirement type="package" version="1.13">gzip</requirement>
         </requirements>
         <version_command><![CDATA[baredSC_1d --version]]></version_command>
     </xml>

diff --git a/tools/dexseq/dexseq_count.xml b/tools/dexseq/dexseq_count.xml
@@ -16,18 +16,20 @@
     <command><![CDATA[
 #if $mode.mode_select == "prepare":
     dexseq_prepare_annotation.py
-        -r $mode.aggregate
-        '$mode.gtffile'
+        -r '${mode.aggregate}'
+        '${mode.gtffile}'
         '$flattened_gtf_out'
 #elif $mode.mode_select == "count":
+    ln -s -f '${mode.bamfile}' 'input.bam' &&
+    ln -s -f '${mode.bamfile.metadata.bam_index}' 'input.bam.bai' &&
     dexseq_count.py
         --format bam
-        --paired $mode.paired
-        --stranded $mode.stranded
-        --minaqual $mode.qual
-        --order $mode.order
-        $mode.flattened_gtf_in
-        '$mode.bamfile'
+        --paired '${mode.paired}'
+        --stranded '${mode.stranded}'
+        --minaqual '${mode.qual}'
+        --order '${mode.order}'
+        '${mode.flattened_gtf_in}'
+        'input.bam'
         '$counts_file'
     &&
     sed -i 's/\"//g' '$counts_file'
@@ -73,14 +75,14 @@
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="mode_select" value="prepare" />
             <param name="gtffile" ftype="gff" value="original.gtf"/>
             <param name="aggregate" value="True"/>
             <output name="flattened_gtf_out" ftype="gtf" compare="sim_size" file="flattened.gtf"/>
         </test>
         <!-- Ensure count mode works -->
-        <test>
+        <test expect_num_outputs="1">
             <param name="mode_select" value="count" />
             <param name="bamfile" ftype="bam" value="in.bam" />
             <param name="flattened_gtf_in" ftype="gff" value="flattened.gtf"/>

diff --git a/tools/dexseq/macros.xml b/tools/dexseq/macros.xml
@@ -1,12 +1,11 @@
-<?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.44</token>
+    <token name="@TOOL_VERSION@">1.48.0</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">22.01</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bioconductor-dexseq</requirement>
-            <requirement type="package" version="1.20.3">r-getopt</requirement>
+            <requirement type="package" version="1.20.4">r-getopt</requirement>
             <requirement type="package" version="0.2.21">r-rjson</requirement>
         </requirements>
     </xml>

diff --git a/tools/dimet/dimet_pca_analysis.xml b/tools/dimet/dimet_pca_analysis.xml
@@ -64,18 +64,18 @@
             <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/>
             <param name="conditions" value='Control,L-Cycloserine'/>
             <output_collection name="report" type="list" count="12">
-                <element file="abundances--cell_pc.csv"  name="abundances--cell_pc.csv" ftype="tabular"/>
-                <element file="abundances--cell_var.csv" name="abundances--cell_var.csv" ftype="tabular"/>
-                <element file="abundances--med_pc.csv" name="abundances--med_pc.csv" ftype="tabular"/>
-                <element file="abundances--med_var.csv" name="abundances--med_var.csv" ftype="tabular"/>
-                <element file="abundances--T0--cell_pc.csv"  name="abundances--T0--cell_pc.csv" ftype="tabular"/>
-                <element file="abundances--T0--cell_var.csv" name="abundances--T0--cell_var.csv" ftype="tabular"/>
-                <element file="abundances--T0--med_pc.csv" name="abundances--T0--med_pc.csv" ftype="tabular"/>
-                <element file="abundances--T0--med_var.csv" name="abundances--T0--med_var.csv" ftype="tabular"/>
-                <element file="abundances--T2h--cell_pc.csv"  name="abundances--T2h--cell_pc.csv" ftype="tabular"/>
-                <element file="abundances--T2h--cell_var.csv" name="abundances--T2h--cell_var.csv" ftype="tabular"/>
-                <element file="abundances--T2h--med_pc.csv" name="abundances--T2h--med_pc.csv" ftype="tabular"/>
-                <element file="abundances--T2h--med_var.csv" name="abundances--T2h--med_var.csv" ftype="tabular"/>
+                <element file="abundances--cell_pc.tsv"  name="abundances--cell_pc.tsv" ftype="tabular"/>
+                <element file="abundances--cell_var.tsv" name="abundances--cell_var.tsv" ftype="tabular"/>
+                <element file="abundances--med_pc.tsv" name="abundances--med_pc.tsv" ftype="tabular"/>
+                <element file="abundances--med_var.tsv" name="abundances--med_var.tsv" ftype="tabular"/>
+                <element file="abundances--T0--cell_pc.tsv"  name="abundances--T0--cell_pc.tsv" ftype="tabular"/>
+                <element file="abundances--T0--cell_var.tsv" name="abundances--T0--cell_var.tsv" ftype="tabular"/>
+                <element file="abundances--T0--med_pc.tsv" name="abundances--T0--med_pc.tsv" ftype="tabular"/>
+                <element file="abundances--T0--med_var.tsv" name="abundances--T0--med_var.tsv" ftype="tabular"/>
+                <element file="abundances--T2h--cell_pc.tsv"  name="abundances--T2h--cell_pc.tsv" ftype="tabular"/>
+                <element file="abundances--T2h--cell_var.tsv" name="abundances--T2h--cell_var.tsv" ftype="tabular"/>
+                <element file="abundances--T2h--med_pc.tsv" name="abundances--T2h--med_pc.tsv" ftype="tabular"/>
+                <element file="abundances--T2h--med_var.tsv" name="abundances--T2h--med_var.tsv" ftype="tabular"/>
             </output_collection>
         </test>
     </tests>

diff --git a/tools/dimet/macros.xml b/tools/dimet/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.2.2</token>
+    <token name="@TOOL_VERSION@">0.2.4</token>
     <token name="@VERSION_SUFFIX@">1</token>
     <token name="@EXECUTABLE@">pca</token>
     <xml name="requirements">
@@ -11,6 +11,12 @@
         <param name="stat_test" type="select" value="KW"  display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
             <option value="KW">Kruskal-Wallis</option>
         </param>
+    </xml>
+     <xml name="statistical_test_for_bivariate_analysis">
+        <param name="stat_test" type="select" value="pearson"  display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
+            <option value="pearson">pearson</option>
+            <option value="spearman">spearman</option>
+        </param>
     </xml>
     <xml name="statistical_test">
         <conditional name="statistics">
@@ -166,6 +172,7 @@
             </when>
         </conditional>
         <expand macro="metadata_file_macros"/>
+        <expand macro="statistical_test_for_bivariate_analysis"/>
     </xml>
     <xml name="input_parameters_diff_analysis">
         <conditional name="data_input">
@@ -638,14 +645,23 @@
     #if $metadata_path:
         ln -s '$metadata_path' data/metadata.csv &&
     #end if
+
+
     #set conditions_MDV_comparison  = {}
-    #silent $conditions_MDV_comparison['isotopologue_proportions']='pearson'
     #set timepoints_MDV_comparison  = {}
-    #silent $timepoints_MDV_comparison['isotopologue_proportions']='pearson'
     #set conditions_metabolite_time_profiles  = {}
-    #silent $conditions_metabolite_time_profiles['abundances']='pearson'
-    #silent $conditions_metabolite_time_profiles['mean_enrichment']='pearson'
 
+    #if str( $stat_test ) == "pearson":
+        #silent $conditions_MDV_comparison['isotopologue_proportions']='pearson'
+        #silent $timepoints_MDV_comparison['isotopologue_proportions']='pearson'
+        #silent $conditions_metabolite_time_profiles['abundances']='pearson'
+        #silent $conditions_metabolite_time_profiles['mean_enrichment']='pearson'
+    #else
+        #silent $conditions_MDV_comparison['isotopologue_proportions']='spearman'
+        #silent $timepoints_MDV_comparison['isotopologue_proportions']='spearman'
+        #silent $conditions_metabolite_time_profiles['abundances']='spearman'
+        #silent $conditions_metabolite_time_profiles['mean_enrichment']='spearman'
+    #end if
     #set $impute_values  = {}
     #if str( $data_input.data_input_selector ) == "abundance":
         #if $data_input.abundance_file: