Mercurial > repos > iuc > stacks2_clonefilter
view stacks_clonefilter.xml @ 1:b75174403a65 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
author | iuc |
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date | Mon, 30 Sep 2019 14:19:47 -0400 |
parents | 1b6d07160736 |
children | 2f1d464ebfd2 |
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<tool id="stacks2_clonefilter" name="Stacks2: clone filter" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@"> <description>Identify PCR clones</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="version_cmd"/> <command detect_errors="aggressive"><![CDATA[ @FASTQ_INPUT_FUNCTIONS@ mkdir stacks_inputs stacks_outputs && #set ($link_command, $fwd_path, $rev_path, $inputype) = $fastq_input_batch($input_type.fqinputs, $input_type.input_type_select) $link_command clone_filter #if $input_type.input_type_select == 'single': -f '$fwd_path' #else -1 '$fwd_path' -2 '$rev_path' #end if -i $inputype -o stacks_outputs $capture $input_type.barcode_encoding #if $oligo_len_1 --oligo_len_1 $oligo_len_1 #end if #if $oligo_len_2 --oligo_len_2 $oligo_len_2 #end if $retain_oligo ## only supports fastq.gz output since the ## the program outputs empty files for fasta/fastq -y gzfastq @TEE_APPEND_LOG@ @CAT_LOG_TO_STDERR@ ## move outputs such that Galaxy can find them #if $capture: #if $input_type.input_type_select == "single" && mv stacks_outputs/*.discards.fq.gz '$discarded' #else && mv stacks_outputs/*.discards.1.fq.gz '$discarded_pair.forward' && mv stacks_outputs/*.discards.2.fq.gz '$discarded_pair.reverse' #end if #end if #if $input_type.input_type_select == "single" && mv stacks_outputs/*.fq.gz '$clean' #else && mv stacks_outputs/*.1.fq.gz '$clean_pair.forward' && mv stacks_outputs/*.2.fq.gz '$clean_pair.reverse' #end if ]]></command> <inputs> <expand macro="fastq_input_bc"/> <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" /> <param name="oligo_len_1" type="integer" value="0" label="Length of the single-end oligo sequence in dataset"/> <param name="oligo_len_2" optional="true" type="integer" label="Length of the paired-end oligo sequence in dataset"/> <param argument="--retain_oligo" type="boolean" checked="false" truevalue="--retain_oligo" falsevalue="" label="Do not trim off the random oligo sequence (if oligo is inline)" /> <expand macro="in_log"/> </inputs> <outputs> <expand macro="out_log"/> <data format="fastqsanger.gz" name="clean" from_work_dir="outputs/R1.fq.gz" label="${tool.name} on ${on_string}"> <filter>input_type['input_type_select'] == 'single'</filter> </data> <collection name="clean_pair" type="paired" label="${tool.name} on ${on_string}"> <filter>input_type['input_type_select'] == 'paired'</filter> </collection> <data name="discarded" format="fastqsanger" label="${tool.name} on ${on_string}: discarded reads"> <filter>capture and input_type['input_type_select'] == 'single' and not options_kmer_char['k_dist']</filter> </data> <collection name="discarded_pair" type="paired" label="${tool.name} on ${on_string}: discarded reads"> <filter>capture and input_type['input_type_select'] == 'paired' and not options_kmer_char['k_dist']</filter> </collection> </outputs> <tests> <!-- single end, defaults--> <test> <conditional name="input_type"> <param name="input_type_select" value="single" /> <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> </conditional> <param name="oligo_len_1" value="6" /> <param name="add_log" value="yes" /> <output name="output_log" ftype="txt" file="clonefilter/clonefilter.log" lines_diff="8"/> <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/> </test> <!-- single end, alt BCencoding, capture--> <test> <conditional name="input_type"> <param name="input_type_select" value="single" /> <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> <param name="barcode_encoding" value="--index_null" /> </conditional> <param name="capture" value="-D" /> <param name="oligo_len_1" value="6" /> <assert_command> <has_text text="-D" /> </assert_command> <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> <output name="discarded" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> </test> <!-- paired end, defaults--> <test> <conditional name="input_type"> <param name="input_type_select" value="paired" /> <param name="fqinputs"> <collection type="paired"> <element name="forward" value="clonefilter/R1_0001.1.fq.gz" /> <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" /> </collection> </param> </conditional> <param name="oligo_len_1" value="6" /> <output_collection name="clean_pair" type="paired"> <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" /> <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" /> </output_collection> </test> <!-- paired end, non defaults --> <test> <conditional name="input_type"> <param name="input_type_select" value="paired" /> <param name="fqinputs"> <collection type="paired"> <element name="forward" value="clonefilter/R1_0001.1.fq.gz" /> <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" /> </collection> </param> </conditional> <param name="oligo_len_1" value="6" /> <param name="capture" value="-D" /> <param name="retain_oligo" value="--retain_oligo" /> <assert_command> <has_text text="--retain_oligo" /> </assert_command> <output_collection name="clean_pair" type="paired"> <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" /> <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" /> </output_collection> <output_collection name="discarded_pair" type="paired"> <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" /> <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" /> </output_collection> </test> </tests> <help> <![CDATA[ .. class:: infomark The clone_filter program is designed to identify PCR clones. @STACKS_INFOS@ ]]> </help> <expand macro="citation" /> </tool>