Mercurial > repos > brenninc > tagdust_2_31
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/paired.xml Mon May 09 04:08:01 2016 -0400 @@ -0,0 +1,95 @@ +<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>