# HG changeset patch
# User p.lucas
# Date 1707831541 0
# Node ID 1acaa51b2b97e02e678eff58ba1f3c4684ff14a4

Uploaded wrapper

diff -r 000000000000 -r 1acaa51b2b97 SsuisSerotyping_pipeline.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SsuisSerotyping_pipeline.xml	Tue Feb 13 13:39:01 2024 +0000
@@ -0,0 +1,158 @@
+<tool id="SsuisSerotyping_pipeline" name="Use SsuisSerotyping_pipeline." version="0.1.2">
+    <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 '$typeofdata.reverse'
+            #else:
+                            --ends se 
+            #end if
+
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="fastq" />
+        <conditional name="optionalfiles">
+           <param name="analysis_selector" type="select" label="Use specific or default configuration?">
+               <option value="default" selected="True">Use default configuration.</option>
+               <option value="specific">Use specific file</option>
+           </param>
+           <when value="default" />
+           <when value="specific">
+               <param type="data" name="serotype_db" format="fasta" label="Serotype database in fasta format." />
+               <param type="data" name="serotype_definitions" format="txt" label="Definition of the serotype database" />
+               <param type="data" name="cps2K" format="fasta" label="Multifasta with cpsH confirmation database" />
+               <param type="data" name="Virulence_db" format="fasta" label="Virulence genes" />
+               <param type="data" name="recN_db" format="fasta" label="recN species specfic gene" />
+               <param type="data" name="MLST_definitions" format="txt" label="Definitions of MLST database file" />
+               <param type="data" name="MLST_db" format="fasta" label="MLST database" />
+           </when>
+        </conditional>
+        <conditional name="typeofdata">
+           <param name="pors" type="select" label="Read option">
+               <option value="single" selected="True">Single-end</option>
+               <option value="paired">Paired-end</option>
+           </param>
+           <when value="single" />
+           <when value="paired">
+               <param type="text" name="reverse" value="_R1" />
+               <param type="text" name="forward" value="_R2" />
+           </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output1" format="txt" label="${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[
+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
+
+--fastq_directory       Path to directory containing paired-end fastq files.
+                        Must be full path to directory, please do not use '.'
+                        or '..' to declare path
+                        If no path is given, the current working
+                        directory is used
+--scoreName             Name of SRST2 results file
+                        [optional: default name 'Results']
+--serotype_db           Multifasta file containing the serotype database
+                        (Ssuis_Serotyping.fasta)
+                        [If none is provided, Ssuis_Serotyping.fasta is looked
+                        for in the directory containing the script]
+--serotype_definitions  Text file containing the definitions for the
+                        serotype database file
+                        (Ssuis_Serotyping_Definitions.txt)
+                        [If none is provided, Ssuis_Serotyping_Definitions.txt is looked
+                        for in the directory containing the script]
+--cps2K         Multifasta file containing the cpsH confirmation database
+                        (Ssuis_cps2K.fasta)
+                        [If none is provided, Ssuis_cps2K.fasta is looked
+                        for in the directory containing the script]
+--MLST_db               Multifasta file containing the MLST database
+                        (Streptococcus_suis.fasta)
+                        [If none is provided, Streptococcus_suis.fasta is looked
+                        for in the directory containing the script]
+--MLST_definitions      Text file containing the definitions for the
+                        MLST database file
+                        (ssuis.txt)
+                        [If none is provided, ssuis.txt is looked
+                        for in the directory containing the script]
+--recN_db               Fasta file containing the recN species specfic gene
+                        (recN_Full.fasta)
+                        [If none is provided, recN_full.fasta is looked
+                        for in the directory containing the script]
+--Virulence_db          Multifasta file containing the Virulence genes
+                        (Virulence.fasta)
+                        [If none is provided, Virulence.fasta is looked
+                        for in the directory containing the script]
+--forward               Indicator delimiting the forward reads file for
+                        paired read fastq files
+
+This option is ignored if single-end reads is selected
+                        [optional: default '_R1']
+
+--reverse               Indicator delimiting the reverse reads file for
+                        paired read fastq files
+
+This option is ignored if single-end reads is selected
+                        [optional: default '_R2']
+
+--ends          Indicates whether the reads are paired-end (pe) or single-end (se)
+                        [optional: default 'pe']
+
+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">
+@misc{githubSsuisSerotyping_pipeline,
+  author = {LastTODO, FirstTODO},
+  year = {TODO},
+  title = {SsuisSerotyping_pipeline},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/streplab/SsuisSerotyping_pipeline},
+}</citation>
+    </citations>
+</tool>