Mercurial > repos > bvalot > pymlst
diff clamlst_search.xml @ 1:5b2c48fa0175 draft
planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
| author | bvalot |
|---|---|
| date | Wed, 07 Dec 2022 15:25:06 +0000 |
| parents | a3cc35af3635 |
| children |
line wrap: on
line diff
--- a/clamlst_search.xml Thu Jun 16 12:32:28 2022 +0000 +++ b/clamlst_search.xml Wed Dec 07 15:25:06 2022 +0000 @@ -1,14 +1,18 @@ -<tool id="clamlst_search_wrapper" name="Search MLST database" version="2.1.3"> +<tool id="clamlst_search_wrapper" name="Search MLST database" + version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> <description></description> - <requirements> - <requirement type="package" version="2.1.3">pymlst</requirement> + <macros> + <import>macro.xml</import> + </macros> + <expand macro="requirements"> <requirement type="package" version="4.8">sed</requirement> - </requirements> + </expand> <stdio> <exit_code range="1:" level="fatal" /> </stdio> <version_command>claMLST -v</version_command> <command><![CDATA[ + #set $databaselink = $database.file_name.split("/")[-1] ln -s $database.file_name \$_GALAXY_JOB_TMP_DIR/ && claMLST #if $data.input == "fasta" @@ -26,37 +30,52 @@ -f '${fastaout}' #end if #if $data.input == "fasta" - \$_GALAXY_JOB_TMP_DIR/`echo $database.file_name | sed -e '~s/.*\///'` '${data.fastain}' - | sed -e "~s/`echo $data.fastain.file_name | sed -e '~s/.*\///' | - sed -e '~s/.dat$//'`/$data.fastain.name/" + \$_GALAXY_JOB_TMP_DIR/'${databaselink}' + #for $datain in $data.fastain: + '${datain}' + #end for + #for $datain in $data.fastain: + #set $name = $datain.file_name.split("/")[-1].rstrip(".dat") + | sed -e "~s/$name/$datain.name/" + #end for #end if #if $data.input == "fastqsingle" #if str($data.reads) -r $data.reads #end if --single - \$_GALAXY_JOB_TMP_DIR/`echo $database.file_name | sed -e '~s/.*\///'` '${data.single}' - | sed -e "~s/`echo $data.single.file_name | sed -e '~s/.*\///' - | sed -e '~s/.dat$//'`/$data.single.name/" + \$_GALAXY_JOB_TMP_DIR/'${databaselink}' + #for $datain in $data.single: + '${datain}' + #end for + #for $datain in $data.single: + #set $name = $datain.file_name.split("/")[-1].rstrip(".dat") + | sed -e "~s/$name/$datain.name/" + #end for #end if #if $data.input == "fastqpaired" #if str($data.reads) -r $data.reads #end if - --paired - \$_GALAXY_JOB_TMP_DIR/`echo $database.file_name | sed -e '~s/.*\///'` '${data.forward}' '${data.reverse}' - | sed -e "~s/`echo $data.forward.file_name | sed -e '~s/.*\///' - | sed -e '~s/.dat$//'`/$data.forward.name/" + --paired + \$_GALAXY_JOB_TMP_DIR/'${databaselink}' + '${data.pairedfile.forward}' '${data.pairedfile.reverse}' + #set $name = $data.pairedfile.forward.file_name.split("/")[-1].rstrip(".dat") + | sed -e "~s/$name/$data.pairedfile.name/" #end if #if $data.input == "fastqpaired2" #if str($data.reads) -r $data.reads #end if - --paired - \$_GALAXY_JOB_TMP_DIR/`echo $database.file_name | sed -e '~s/.*\///'` '${data.pairedfile.forward}' - '${data.pairedfile.reverse}' - | sed -e "~s/`echo $data.pairedfile.forward.file_name | sed -e '~s/.*\///' - | sed -e '~s/.dat$//'`/$data.pairedfile.name/" + --paired + \$_GALAXY_JOB_TMP_DIR/'${databaselink}' + #for $datain in $data.pairedfilelist: + '${datain.forward}' '${datain.reverse}' + #end for + #for $datain in $data.pairedfilelist: + #set $name = $datain.forward.file_name.split("/")[-1].rstrip(".dat") + | sed -e "~s/$name/$datain.name/" + #end for #end if > '${mlst}' #if $log @@ -73,33 +92,34 @@ <param name="input" type="select" label="Select type of data"> <option value="fasta" selected="true">Assembly (fasta)</option> <option value="fastqsingle">Raw data (single)</option> - <option value="fastqpaired">Raw data (paired separated)</option> - <option value="fastqpaired2">Raw data (paired)</option> + <option value="fastqpaired">Raw data (paired)</option> + <option value="fastqpaired2">Raw data (List of paired)</option> </param> <when value="fasta"> <param name="fastain" type="data" format="fasta" - label="Assembly Genome" help="Fasta format" /> + label="Assembly Genome" help="Fasta format" + multiple="true" /> </when> <when value="fastqsingle"> <param name="single" type="data" format="fastq,fastq.gz" - label="Single read file" help="Fastq(gz) format" /> + label="Single read file" help="Fastq(gz) format" + multiple="true" /> <param name="reads" type="integer" value="10" optional="true" label="Minimum reads coverage to search gene" /> </when> <when value="fastqpaired"> - <param name="forward" type="data" format="fastq,fastq.gz" - label="Forward read file" help="Fastq(gz) format" /> - <param name="reverse" type="data" format="fastq,fastq.gz" - label="Reverse read file" help="Fastq(gz) format" /> - <param name="reads" type="integer" value="10" optional="true" - label="Minimum reads coverage to search gene" /> - </when> - <when value="fastqpaired2"> <param name="pairedfile" type="data_collection" format="fastq,fastq.gz" label="Paired of read files" help="Fastq(gz) format" collection_type="paired" /> <param name="reads" type="integer" value="10" optional="true" label="Minimum reads coverage to search gene" /> + </when> + <when value="fastqpaired2"> + <param name="pairedfilelist" type="data_collection" format="fastq,fastq.gz" + label="Paired of read files" help="Fastq(gz) format" + collection_type="list:paired" /> + <param name="reads" type="integer" value="10" optional="true" + label="Minimum reads coverage to search gene" /> </when> </conditional> <param name="fasta" type="boolean" checked="false" @@ -127,36 +147,77 @@ <param name="database" value="clamlst_ecoli.db" /> <conditional name="data"> <param name="input" value="fasta" /> - <param name="fastain" ftype="fasta" value="EHSB-021.fasta" /> + <param name="fastain" ftype="fasta" value="EHSB-021.fasta,EHSB-092.fasta" /> </conditional> <param name="identity" value="0.8" /> <output name="mlst" ftype="txt"> <assert_contents> <has_text_matching expression="155\t6\t4\t14\t16\t24\t8\t14" /> + <has_text_matching expression="3018\t12\t58\t54\t344\t1\t2\t47" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="database" value="clamlst_ecoli.db" /> + <conditional name="data"> + <param name="input" value="fastqsingle" /> + <param name="single" ftype="fastqsanger" value="EHSB-021_R1.fastq.gz,EHSB-021_R2.fastq.gz" /> + </conditional> + <param name="identity" value="0.8" /> + <param name="reads" value="5" /> + <output name="mlst" ftype="txt"> + <assert_contents> + <has_text_matching expression="14\t16\t24\t8" /> </assert_contents> </output> </test> - <!-- <test expect_num_outputs="3"> --> - <!-- <param name="database" value="clamlst_ecoli.db" /> --> - <!-- <conditional name="data"> --> - <!-- <param name="input" value="fastqpaired" /> --> - <!-- <param name="forward" ftype="fastq.gz" value="EHSB-021_R1.fastq.gz" /> --> - <!-- <param name="reverse" ftype="fastq.gz" value="EHSB-021_R2.fastq.gz" /> --> - <!-- <param name="reads" value="5" /> --> - <!-- </conditional> --> - <!-- <param name="fasta" value="true" /> --> - <!-- <param name="log" value="true" /> --> - <!-- <output name="fastaout" ftype="fasta"> --> - <!-- <assert_contents> --> - <!-- <has_n_lines n="14" /> --> - <!-- </assert_contents> --> - <!-- </output> --> - <!-- <output name="mlst" ftype="txt"> --> - <!-- <assert_contents> --> - <!-- <has_text_matching expression="4\t14\t16\t24\t8\t14" /> --> - <!-- </assert_contents> --> - <!-- </output> --> - <!-- </test> --> + <test expect_num_outputs="1"> + <param name="database" value="clamlst_ecoli.db" /> + <conditional name="data"> + <param name="input" value="fastqpaired" /> + <param name="pairedfile"> + <collection type="paired"> + <element name="forward" value="EHSB-021_R1.fastq.gz" /> + <element name="reverse" value="EHSB-021_R2.fastq.gz" /> + </collection> + </param> + <param name="reads" value="5" /> + </conditional> + <output name="mlst" ftype="txt"> + <assert_contents> + <has_text_matching expression="4\t14\t16\t24\t8\t14" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <param name="database" value="clamlst_ecoli.db" /> + <conditional name="data"> + <param name="input" value="fastqpaired2" /> + <param name="pairedfilelist"> + <collection type="list:paired"> + <element name="EHSB-021"> + <collection type="paired"> + <element name="forward" value="EHSB-021_R1.fastq.gz" /> + <element name="reverse" value="EHSB-021_R2.fastq.gz" /> + </collection> + </element> + </collection> + </param> + <param name="reads" value="5" /> + </conditional> + <param name="fasta" value="true" /> + <param name="log" value="true" /> + <output name="fastaout" ftype="fasta"> + <assert_contents> + <has_n_lines n="14" /> + </assert_contents> + </output> + <output name="mlst" ftype="txt"> + <assert_contents> + <has_text_matching expression="4\t14\t16\t24\t8\t14" /> + </assert_contents> + </output> + </test> </tests> <help> **What it does**