Mercurial > repos > drosofff > msp_sr_bowtie_parser

comparison sRbowtieParser.xml @ 15:a39761c27e77 draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Mon, 29 Jun 2015 05:54:17 -0400
parents 115af29c4f57
children bfeaf4415eba
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14:115af29c4f57 15:a39761c27e77
1 <tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.5"> 1 <tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.5">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.12.7">bowtie</requirement> 4 <requirement type="package" version="0.12.7">bowtie</requirement>
5 <requirement type="package" version="1.2">samtools</requirement>
6 <requirement type="package" version="0.7.7">pysam</requirement> 5 <requirement type="package" version="0.7.7">pysam</requirement>
7 <requirement type="package" version="1.9">numpy</requirement> 6 <requirement type="package" version="1.9">numpy</requirement>
8 </requirements> 7 </requirements>
9 <command interpreter="python"> 8 <command interpreter="python">
10 sRbowtieParser.py 9 sRbowtieParser.py
37 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> 36 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
38 <option value="indexed">Use a built-in index</option> 37 <option value="indexed">Use a built-in index</option>
39 <option value="history">Use one from the history</option> 38 <option value="history">Use one from the history</option>
40 </param> 39 </param>
41 <when value="indexed"> 40 <when value="indexed">
42 <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"> 41 <param name="input_list" type="data" format="tabular,sam,bam" label="Select multiple alignments to parse" multiple="true">
43 <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/> 42 <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/>
44 </param> 43 </param>
45 </when> 44 </when>
46 <when value="history"> 45 <when value="history">
47 <param name="ownFile" type="data" format="fasta" label="Select the fasta reference" /> 46 <param name="ownFile" type="data" format="fasta" label="Select the fasta reference" />
48 <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"/> 47 <param name="input_list" type="data" format="tabular,sam,bam" label="Select multiple alignments to parse" multiple="true"/>
49 </when> 48 </when>
50 </conditional> <!-- refGenomeSource --> 49 </conditional> <!-- refGenomeSource -->
51 <param name="polarity" type="select" label="how to count sense and antisense reads"> 50 <param name="polarity" type="select" label="how to count sense and antisense reads">
52 <option value="both">count both sense and antisense reads</option> 51 <option value="both">count both sense and antisense reads</option>
53 <option value="forward">count only sense reads</option> 52 <option value="forward">count only sense reads</option>