# HG changeset patch
# User p.lucas
# Date 1723104070 0
# Node ID 76c82b2a43d23957b85fb5911b9f5719d26c9914
# Parent  99dae22a6fde70b55d8cae29560c8f787fe583a0
Uploaded

diff -r 99dae22a6fde -r 76c82b2a43d2 SsuisSerotyping_pipeline.xml
--- a/SsuisSerotyping_pipeline.xml	Thu Aug 08 07:40:51 2024 +0000
+++ b/SsuisSerotyping_pipeline.xml	Thu Aug 08 08:01:10 2024 +0000
@@ -1,89 +1,93 @@
-<tool id="SsuisSerotyping_pipeline" name="Use SsuisSerotyping_pipeline." version="0.1.4">
-    <requirements>
-        <requirement type="package">perl-bioperl</requirement>
-        <requirement type="package">scipy</requirement>
-        <requirement type="package" version="2.7">python</requirement>
-        <requirement type="package">srst2</requirement>
-    </requirements>
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
-    <command><![CDATA[
-        python $__tool_directory__/Prepare_Ssuis_serotypingPipeline.py 
-            --fastq_file $input1  
-            --scoreName '$output1'
-            --output2 '$output2'
-            --output3 '$output3'
-            --output4 '$output4'
-            --output5 '$output5'
-            --output6 '$output6'
-            --output7 '$output7'
-            --output8 '$output8'
-            #if $optionalfiles.analysis_selector == "specific":
-                            --serotype_db '$options.serotype_db' 
-                            --serotype_definitions '$options.serotype_definitions' 
-                            --cps2K '$options.cps2K' 
-                            --Virulence_db '$options.Virulence_db' 
-                            --recN_db '$options.recN_db' 
-                            --MLST_definitions '$options.MLST_definitions' 
-                            --MLST_db '$options.MLST_db'
-            #end if
-            #if $typeofdata.pors == "paired":
-                            --ends pe
-                            --forward '$typeofdata.forward'
-                            --reverse '$typeofdata.reverse'
-            #else:
-                            --ends se 
-            #end if
-
-    ]]></command>
-    <inputs>
+<tool id="SsuisSerotyping_pipeline" name="Use SsuisSerotyping_pipeline." version="0.1.5">
+  <requirements>
+    <requirement type="package">perl-bioperl</requirement>
+    <requirement type="package">scipy</requirement>
+    <requirement type="package" version="2.7">python</requirement>
+    <requirement type="package">srst2</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+  <command><![CDATA[
+    python $__tool_directory__/Prepare_Ssuis_serotypingPipeline.py 
+      --scoreName '$output1'
+      --output2 '$output2'
+      --output3 '$output3'
+      --output4 '$output4'
+      --output5 '$output5'
+      --output6 '$output6'
+      --output7 '$output7'
+      --output8 '$output8'
+      #if $optionalfiles.analysis_selector == "specific":
+        --serotype_db '$options.serotype_db' 
+        --serotype_definitions '$options.serotype_definitions' 
+        --cps2K '$options.cps2K' 
+        --Virulence_db '$options.Virulence_db' 
+        --recN_db '$options.recN_db' 
+        --MLST_definitions '$options.MLST_definitions' 
+        --MLST_db '$options.MLST_db'
+      #end if
+      #if $typeofdata.pors == "paired":
+        --ends pe
+        --forward '$typeofdata.forward'
+        --reverse '$typeofdata.reverse'
+        --fastq_file $input1 
+        --fastq_file2 $input2 
+      #else:
+        --ends se 
+        --fastq_file $input1 
+      #end if
+  ]]></command>
+  <inputs>
+    <conditional name="optionalfiles">
+      <param name="analysis_selector" type="select" label="Use specific or default configuration?">
+        <option value="default" selected="True">Use default configuration.</option>
+        <option value="specific">Use specific file</option>
+      </param>
+      <when value="default" />
+      <when value="specific">
+        <param type="data" name="serotype_db" format="fasta" label="Serotype database in fasta format." />
+        <param type="data" name="serotype_definitions" format="txt" label="Definition of the serotype database" />
+        <param type="data" name="cps2K" format="fasta" label="Multifasta with cpsH confirmation database" />
+        <param type="data" name="Virulence_db" format="fasta" label="Virulence genes" />
+        <param type="data" name="recN_db" format="fasta" label="recN species specfic gene" />
+        <param type="data" name="MLST_definitions" format="txt" label="Definitions of MLST database file" />
+        <param type="data" name="MLST_db" format="fasta" label="MLST database" />
+      </when>
+    </conditional>
+    <conditional name="typeofdata">
+      <param name="pors" type="select" label="Read option">
+        <option value="single" selected="True">Single-end</option>
+        <option value="paired">Paired-end</option>
+      </param>
+      <when value="single">
         <param type="data" name="input1" format="fastq" />
-        <conditional name="optionalfiles">
-           <param name="analysis_selector" type="select" label="Use specific or default configuration?">
-               <option value="default" selected="True">Use default configuration.</option>
-               <option value="specific">Use specific file</option>
-           </param>
-           <when value="default" />
-           <when value="specific">
-               <param type="data" name="serotype_db" format="fasta" label="Serotype database in fasta format." />
-               <param type="data" name="serotype_definitions" format="txt" label="Definition of the serotype database" />
-               <param type="data" name="cps2K" format="fasta" label="Multifasta with cpsH confirmation database" />
-               <param type="data" name="Virulence_db" format="fasta" label="Virulence genes" />
-               <param type="data" name="recN_db" format="fasta" label="recN species specfic gene" />
-               <param type="data" name="MLST_definitions" format="txt" label="Definitions of MLST database file" />
-               <param type="data" name="MLST_db" format="fasta" label="MLST database" />
-           </when>
-        </conditional>
-        <conditional name="typeofdata">
-           <param name="pors" type="select" label="Read option">
-               <option value="single" selected="True">Single-end</option>
-               <option value="paired">Paired-end</option>
-           </param>
-           <when value="single" />
-           <when value="paired">
-               <param type="text" name="reverse" value="_R1" />
-               <param type="text" name="forward" value="_R2" />
-           </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data name="output1" format="txt" label="${tool.name} on ${on_string}: Results_FinalResults.txt" from_work_dir="Results_FinalResults.txt"/>
-        <data name="output2" format="txt" label="${tool.name} on ${on_string}: Results_MLSTResults.txt" from_work_dir="Results_MLSTResults.txt"/>
-        <data name="output3" format="txt" label="${tool.name} on ${on_string}: Results_recN__fullgenes__recN_full__results.txt" from_work_dir="Results_recN__fullgenes__recN_full__results.txt" />
-        <data name="output4" format="txt" label="${tool.name} on ${on_string}: Results_speciesConfirmation.txt" from_work_dir="Results_speciesConfirmation.txt" />
-        <data name="output5" format="txt" label="${tool.name} on ${on_string}: Results_FinalSerotypingResults.txt" from_work_dir="Results_FinalSerotypingResults.txt" />
-        <data name="output6" format="txt" label="${tool.name} on ${on_string}: Results_InitialCapsuleResults.txt" from_work_dir="Results_InitialCapsuleResults.txt" />
-        <data name="output7" format="txt" label="${tool.name} on ${on_string}: Results_VirulenceFactors__fullgenes__Virulence__results.txt" from_work_dir="Results_VirulenceFactors__fullgenes__Virulence__results.txt" />
-        <data name="output8" format="txt" label="${tool.name} on ${on_string}: Results_VirulenceFactorResults.txt" from_work_dir="Results_VirulenceFactorResults.txt" />
-    </outputs>
-    <tests>
-        <test>
-            <param name="input1" value="/home/plucas/TEST/SsuisSerotyping_pipeline/input_fastq/SS1218_IonXpress_008_R_2016_02_23.soft_clean.trimmomatic_trimmed.fastq"/>
-            <output name="output1" file="/home/plucas/TEST/SsuisSerotyping_pipeline/results/Results_FinalResults.txt"/>
-        </test>
-    </tests>
-    <help><![CDATA[
+      </when>
+      <when value="paired">
+        <param type="text" name="reverse" value="_R1" />
+        <param type="text" name="forward" value="_R2" />
+        <param type="data" name="input1" format="fastq" />
+        <param type="data" name="input2" format="fastq" />
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data name="output1" format="txt" label="${tool.name} on ${on_string}: Results_FinalResults.txt" from_work_dir="Results_FinalResults.txt"/>
+    <data name="output2" format="txt" label="${tool.name} on ${on_string}: Results_MLSTResults.txt" from_work_dir="Results_MLSTResults.txt"/>
+    <data name="output3" format="txt" label="${tool.name} on ${on_string}: Results_recN__fullgenes__recN_full__results.txt" from_work_dir="Results_recN__fullgenes__recN_full__results.txt" />
+    <data name="output4" format="txt" label="${tool.name} on ${on_string}: Results_speciesConfirmation.txt" from_work_dir="Results_speciesConfirmation.txt" />
+    <data name="output5" format="txt" label="${tool.name} on ${on_string}: Results_FinalSerotypingResults.txt" from_work_dir="Results_FinalSerotypingResults.txt" />
+    <data name="output6" format="txt" label="${tool.name} on ${on_string}: Results_InitialCapsuleResults.txt" from_work_dir="Results_InitialCapsuleResults.txt" />
+    <data name="output7" format="txt" label="${tool.name} on ${on_string}: Results_VirulenceFactors__fullgenes__Virulence__results.txt" from_work_dir="Results_VirulenceFactors__fullgenes__Virulence__results.txt" />
+    <data name="output8" format="txt" label="${tool.name} on ${on_string}: Results_VirulenceFactorResults.txt" from_work_dir="Results_VirulenceFactorResults.txt" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="/home/plucas/TEST/SsuisSerotyping_pipeline/input_fastq/SS1218_IonXpress_008_R_2016_02_23.soft_clean.trimmomatic_trimmed.fastq"/>
+      <output name="output1" file="/home/plucas/TEST/SsuisSerotyping_pipeline/results/Results_FinalResults.txt"/>
+    </test>
+  </tests>
+  <help><![CDATA[
 Implementation of the S. suis serotyping pipeline:
 
 perl Ssuis_serotypingPipeline.pl --fastq_directory /path/to/fastq/directory --scoreName Scores_output_name --serotype_db serotype.fasta --serotype_definitions serotype_definitions.txt --cps2K cps2K.fasta
@@ -143,9 +147,9 @@
 Note: We recommend using paired end reads of at least 100nt in length
 and at least 30X coverage.
 We have not tested the efficiency of the pipeline with reads shorter than 80nt.
-    ]]></help>
-    <citations>
-        <citation type="bibtex">
+  ]]></help>
+  <citations>
+    <citation type="bibtex">
 @misc{githubSsuisSerotyping_pipeline,
   author = {LastTODO, FirstTODO},
   year = {TODO},
@@ -153,6 +157,7 @@
   publisher = {GitHub},
   journal = {GitHub repository},
   url = {https://github.com/streplab/SsuisSerotyping_pipeline},
-}</citation>
-    </citations>
+}
+    </citation>
+  </citations>
 </tool>