Mercurial > repos > iuc > stacks_clonefilter
diff stacks_clonefilter.xml @ 0:a8a0cd05d47d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
author | iuc |
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date | Sun, 21 May 2017 18:54:11 -0400 |
parents | |
children | a0a51078cb61 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/stacks_clonefilter.xml Sun May 21 18:54:11 2017 -0400 @@ -0,0 +1,148 @@ +<tool id="stacks_clonefilter" name="Stacks: clone filter" version="@WRAPPER_VERSION@.0"> +<description>Identify PCR clones</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command><![CDATA[ + + #if $data_type.dt_select == "single" + + #if $data_type.fname.is_of_type('fastqsanger') + #set $ext = ".fq" + #set inputype = "fastq" + #else + #set $ext = ".fq.gz" + #set inputype = "gzfastq" + #end if + + ln -s '$data_type.fname' R1$ext && + #else + + #if $data_type.fwd.is_of_type('fastqsanger') + #set $ext = ".fq" + #set inputype = "fastq" + #else + #set $ext = ".fq.gz" + #set inputype = "gzfastq" + #end if + + ln -s '$data_type.fwd' R1$ext && + ln -s '$data_type.rev' R2$ext && + #end if + + + mkdir clone_outputs + + && + + clone_filter + #if $data_type.dt_select == 'single': + -f R1$ext + + #else + -1 R1$ext + -2 R2$ext + #end if + + -i $inputype + + -o clone_outputs + + + #if $oligo_len_1 + --oligo_len_1 $oligo_len_1 + $data_type.barcode_encoding + #end if + #if $oligo_len_2 + --oligo_len_2 $oligo_len_2 + #end if + + -y gzfastq + + ]]></command> + <inputs> + <conditional name="data_type"> + <param name="dt_select" type="select" label="Single or Paired-end"> + <option value="single">Single</option> + <option value="pair">Pair</option> + </param> + <when value="single"> + <param name="fname" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ" /> + <param name="barcode_encoding" type="select" label="Barcode location"> + <expand macro="barcode_encoding_single" /> + </param> + + </when> + <when value="pair"> + <param name="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Forward FASTQ" /> + <param name="rev" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse FASTQ" /> + <param name="barcode_encoding_pair" type="select" label="Barcode location"> + <expand macro="barcode_encoding_single" /> + </param> + </when> + </conditional> + <param name="oligo_len_1" optional="true" type="integer" label="length of the single-end oligo sequence in data set"/> + <param name="oligo_len_2" optional="true" type="integer" label="length of the paired-end oligo sequence in data set"/> + + </inputs> + <outputs> + <data format="fastqsangergz" name="clean" from_work_dir="clone_outputs/R1.fq.gz"> + <filter>data_type['dt_select'] == 'single'</filter> + </data> + + <data format="fastqsangergz" name="clean_fwd" from_work_dir="clone_outputs/R1.1.fq.gz"> + <filter>data_type['dt_select'] == 'pair'</filter> + </data> + <data format="fastqsangergz" name="clean_rev" from_work_dir="clone_outputs/R2.2.fq.gz"> + <filter>data_type['dt_select'] == 'pair'</filter> + </data> + </outputs> + <tests> + <test> + <conditional name="data_type"> + <param name="dt_select" value="single" /> + <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> + </conditional> + <param name="oligo_len_1" value="6" /> + <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/> + </test> + <test> + <conditional name="data_type"> + <param name="dt_select" value="single" /> + <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> + </conditional> + <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> + </test> + <test> + <conditional name="data_type"> + <param name="dt_select" value="pair" /> + <param name="fwd" ftype="fastqsanger" value="clonefilter/R1_0001.1.fq.gz" /> + <param name="rev" ftype="fastqsanger" value="clonefilter/R2_0001.2.fq.gz" /> + </conditional> + <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> + <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/> + </test> + <test> + <conditional name="data_type"> + <param name="dt_select" value="pair" /> + <param name="fwd" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> + <param name="rev" ftype="fastqsanger.gz" value="clonefilter/R2_0001.2.fq.gz" /> + </conditional> + <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> + <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/> + </test> + </tests> + <help> +<![CDATA[ +.. class:: infomark + + +The clone_filter program is designed to identify PCR clones. + +@STACKS_INFOS@ +]]> + </help> + <expand macro="citation" /> +</tool>