Mercurial > repos > brenninc > tagdust_2_31
view paired.xml @ 0:40c86e14b674 draft
Uploaded first version of tagdust
author | brenninc |
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date | Mon, 09 May 2016 04:08:01 -0400 |
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<tool id="tagdust_paired_runner_2_31" name="Tagdust paired end runner" version="0.2"> <description>Runs tagdust in paired end mode</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"></expand> <expand macro="stdio"></expand> <expand macro="version_command"></expand> <command > @cat-archiecture@ cp $read1_file read1.fastq ; cp $read2_file read2.fastq ; @tagdust-call-minus-files@ read1.fastq read2.fastq ; @ls_and_barcode@ </command> <inputs> <param name="read1_file" type="data" format="fastq,fastqsanger" label="Read 1 Fastq file to process" /> <param name="read2_file" type="data" format="fastq,fastqsanger" label="Read 2 Fastq file to process" /> <expand macro="reference_source"/> <expand macro="architecture"/> <expand macro="include_barcode_file"/> <expand macro="architecture"></expand> </inputs> <outputs> <data format="txt" name="logfile" label="Tagdust log on ${on_string}." from_work_dir="output/data_logfile.txt"/> <data format_source="read1_file" name="extracted1" label="Tagdust extracted Read1 from ${on_string}." from_work_dir="output/data_READ1.fq"/> <data format_source="read1_file" name="unextracted1" label="Tagdust un-extracted Read1 from ${on_string}." from_work_dir="output/data_un_READ1.fq"/> <data format_source="read2_file" name="extracted2" label="Tagdust extracted Read2 from ${on_string}." from_work_dir="output/data_READ2.fq"/> <data format_source="read2_file" name="unextracted2" label="Tagdust un-extracted Read2 from ${on_string}." from_work_dir="output/data_un_READ2.fq"/> <expand macro="output_barcode"/> </outputs> <tests> <!-- Large dataset in github but not toolshed --> <test> <param name="read1_file" value="C75_S29_R1_001_extracted.fastq" ftype="fastq" /> <param name="read2_file" value="C75_S29_R2_001_extracted.fastq" ftype="fastq" /> <param name="architecture" value="R:N" /> <param name="reference_source|reference_source_selector" value="history"/> <param name="reference_source|ref_file" value="ercc_and_TPA_mouse_rRNA.fa" ftype="fasta"/> <output name="logfile" > <assert_contents> <has_text text="Determining threshold for read0." /> </assert_contents> </output> <output name="extracted1" file="C75_S29__READ1.fq" compare="sim_size" delta="10000"/> <output name="unextracted1" file="C75_S29__un_READ1.fq" compare="sim_size" delta="10000"/> <output name="extracted2" file="C75_S29__READ2.fq" compare="sim_size" delta="10000"/> <output name="unextracted2" file="C75_S29__un_READ2.fq" compare="sim_size" delta="10000"/> </test> <test> <param name="read1_file" value="read1_extracted.fastq" ftype="fastqsanger" /> <param name="read2_file" value="read2_extracted.fastq" ftype="fastqsanger" /> <param name="architecture" value="test_R:N" /> <param name="reference_source|reference_source_selector" value="history"/> <param name="reference_source|ref_file" value="ercc_and_TPA_mouse_rRNA.fa" ftype="fasta"/> <output name="logfile" > <assert_contents> <has_text text="Determining threshold for read0." /> </assert_contents> </output> <output name="extracted1" file="paired_READ1.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/> <output name="unextracted1" file="paired_un_READ1.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/> <output name="extracted2" file="paired_READ2.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/> <output name="unextracted2" file="paired_un_READ2.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/> </test> <test> <param name="read1_file" value="read1_extracted.fastq" ftype="fastq" /> <param name="read2_file" value="read2_extracted.fastq" ftype="fastq" /> <param name="architecture" value="test_R:N" /> <param name="reference_source|reference_source_selector" value="cached"/> <param name="ref_path" value="test_ercc_and_TPA_mouse_RNA"/> <output name="logfile" > <assert_contents> <has_text text="Determining threshold for read0." /> </assert_contents> </output> <output name="extracted1" file="paired_READ1.fq" compare="sim_size" delta="1000"/> <output name="unextracted1" file="paired_un_READ1.fq" compare="sim_size" delta="1000"/> <output name="extracted2" file="paired_READ2.fq" compare="sim_size" delta="1000"/> <output name="unextracted2" file="paired_un_READ2.fq" compare="sim_size" delta="1000"/> </test> </tests> <help> <![CDATA[ This tool runs Tagdust2 in paired end mode. ]]> @tool-documentation@ @tagdust-documentation@ </help> <expand macro="citations"></expand> </tool>