Mercurial > repos > brenninc > tagdust_2_31
diff single.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/single.xml Mon May 09 04:08:01 2016 -0400 @@ -0,0 +1,87 @@ +<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>