Mercurial > repos > mzeidler > virana2
changeset 10:d042cf2f4043 draft
Uploaded
author | mzeidler |
---|---|
date | Tue, 24 Sep 2013 14:23:49 -0400 |
parents | 312cb1b2d3cd |
children | ed2170329841 |
files | vmap_dnamap.xml |
diffstat | 1 files changed, 12 insertions(+), 14 deletions(-) [+] |
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--- a/vmap_dnamap.xml Tue Sep 24 14:22:46 2013 -0400 +++ b/vmap_dnamap.xml Tue Sep 24 14:23:49 2013 -0400 @@ -7,9 +7,7 @@ <requirement type="package" version="0.1.19">samtools</requirement> <requirement type="package" version="0.7.4">bwa</requirement> <requirement type="package" version="1.0">virana_python</requirement> - <requirement type="package" version="1.7.1">numpy</requirement> - <requirement type="package" version="1.61">biopython</requirement> - <requirement type="package" version="0.5.4">htseq</requirement> + </requirements> <command interpreter="python">vmap.py dnamap @@ -86,24 +84,24 @@ </command> <inputs> - <param name="reads" type="data" format="fastq" label="Read file"/> + <param name="reads" type="data" format="fastq" label="Read file" help="input read file"/> <conditional name="paired"> - <param name="select_paired" type="select" label="Paired end reads?" > + <param name="select_paired" type="select" label="Paired end reads?" help="Set to 'paired end' in case of paired end read input."> <option value="single">single end</option> <option value="paired">paired end</option> </param> <when value="paired"> - <param name="paired_read" type="data" format="fastq" label="Paired end read file" /> + <param name="paired_read" type="data" format="fastq" label="Paired end read file" help="input paired end read file" /> </when> </conditional> <conditional name="output_type"> - <param name="hit" type="boolean" label="Hit Output"/> + <param name="hit" type="boolean" label="Hit Output" help="check this box for output of virana hit file"/> <when value="true"> - <param name="max_mismatches" type="integer" min="0" max="10000000" optional="true" label="Maximum number of mismatches for saved hits"/> + <param name="max_mismatches" type="integer" min="0" max="10000000" optional="true" label="Maximum number of mismatches for saved hits" /> <param name="max_relative_mismatches" type="float" min="0" max="1" optional="true" label="Maximum number of mismatches relative to read length for saved hits " /> <param name="min_continiously_matching" type="integer" min="0" max="10000000" optional="true" label="Minimum number of continious matches for saved hits" /> <param name="min_mapping_score" type="integer" min="1" max="255" optional="true" label="Mimimum mapping score for saved hit" /> @@ -114,12 +112,12 @@ </conditional> - <param name="bam" type="boolean" label="BAM Output"/> - <param name="sam" type="boolean" label="SAM Output"/> - <param name="qual" type="boolean" label="Quality Output"/> - <param name="tax" type="boolean" label="Taxonomy Output"/> + <param name="bam" type="boolean" label="BAM Output" help="check this box for output of unsorted, unindexed BAM file"/> + <param name="sam" type="boolean" label="SAM Output" help="check this box for output of SAM file"/> + <param name="qual" type="boolean" label="Quality Output" help="check this box for output of quality file"/> + <param name="tax" type="boolean" label="Taxonomy Output" help="check this box for output of taxonomy file"/> - <param name="refseq" type="select" label="Set RefSeq taxonomic groups" multiple="true" display="checkboxes" optional="true"> + <param name="refseq" type="select" label="Set RefSeq taxonomic groups" multiple="true" display="checkboxes" optional="true" help="Only generate hit groups that include at last one read mapping to a reference of this reference group"> <option value="UniVec">UniVec</option> <option value="rRNA">rRNA</option> <option value="Homo_sapiens">Homo sapiens</option> @@ -133,7 +131,7 @@ <option value="Bacteria_DRAFT">Bacteria DRAFT</option> </param> - <param name="index" type="data" format="bwa_index" label="BWA Index files"/> + <param name="index" type="data" format="bwa_index" label="BWA Index files" help="BWA Index files to map the reades against."/> <param name="sample_id" type="text" optional="true" label="String used to designate sample information within the hit file"/>