Mercurial > repos > brenninc > tagdust_2_31
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author | brenninc |
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date | Tue, 21 Jun 2016 03:37:10 -0400 |
parents | 40c86e14b674 |
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<tool id="tagdust_single_runner_2_31" name="Tagdust single end runner" version="0.2"> <description>Runs tagdust in single end mode</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> <command > @cat-archiecture@ cp $fastq_file input.fastq ; @tagdust-call-minus-files@ input.fastq ; @ls_and_barcode@ </command> <inputs> <param name="fastq_file" type="data" format="fastq,fastqsanger" label="Fastq file to process" /> <expand macro="reference_source"/> <expand macro="architecture"/> <expand macro="include_barcode_file"/> </inputs> <outputs> <data format="txt" name="logfile" label="Tagdust log on ${on_string} ." from_work_dir="output/data_logfile.txt"/> <data format_source="fastq_file" name="extracted" label="Tagdust extracted reads from ${on_string}." from_work_dir="output/data.fq"/> <data format_source="fastq_file" name="unextracted" label="Tagdust un-extracted reads from ${on_string}." from_work_dir="output/data_un.fq"/> <expand macro="output_barcode"/> </outputs> <tests> <!-- Large dataset in github but not toolshed --> <!--test> <param name="fastq_file" value="C75_S29_R1_001.fastq" ftype="fastq" /> <param name="architecture" value="F:NNNNNNNN_S:TATAGGG_R:N" /> <param name="include|barcode_files" value="no" /> <output name="logfile" > <assert_contents> <has_text text="Determining threshold for read0." /> </assert_contents> </output> <output name="extracted" file="C75_S29_R1_001.fq" compare="sim_size" delta="10000"/> <output name="unextracted" file="C75_S29_R1_001_un.fq" compare="sim_size" delta="10000"/> </test--> <test> <param name="fastq_file" value="read1.fastq" ftype="fastqsanger" /> <param name="architecture" value="test_F:NNNNNNNN_S:TATAGGG_R:N" /> <param name="barcode_files" value="no" /> <output name="logfile" > <assert_contents> <has_text text="Determining threshold for read0." /> </assert_contents> </output> <output name="extracted" file="read1.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/> <output name="unextracted" file="read1_un.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/> </test> <test> <param name="run_type_selector" value="single"/> <param name="fastq_file" value="read1.fastq" ftype="fastq" /> <param name="architecture" value="test_B:GTA_AAC_R:N" /> <param name="include|barcode_files" value="yes" /> <output name="logfile" > <assert_contents> <has_text text="Determining threshold for read0." /> </assert_contents> </output> <output name="extracted" file="with_b_.fq"/> <output name="unextracted" file="with_b_un.fq"/> <output name="barcode_files"> <assert_contents> <has_line line="data_BC_AAC.fq" /> <has_line line="data_BC_GTA.fq" /> </assert_contents> <discovered_dataset designation="AAC" ftype="fastq" file="with_b_BC_AAC.fq"/> <discovered_dataset designation="GTA" ftype="fastq" file="with_b_BC_GTA.fq"/> </output> </test> </tests> <help> <![CDATA[ This tool runs Tagdust2 in single mode. ]]> @tool-documentation@ @tagdust-documentation@ </help> <expand macro="citations"></expand> </tool>