Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms

comparison readmap.xml @ 20:45df4c72a780 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 521b1e3fcf3dbf9d61d6b2b90d2415c3dadc4b5a
author drosofff
date Wed, 26 Sep 2018 11:06:34 -0400
parents 675033bcb79e
children
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19:675033bcb79e 20:45df4c72a780
1 <tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.2.7.3"> 1 <tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.2.7.4">
2 <description>from sRbowtie aligment</description> 2 <description>from sRbowtie aligment</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1.2=py27_0">bowtie</requirement> 4 <requirement type="package" version="1.1.2=py27_0">bowtie</requirement>
5 <requirement type="package" version="1.11.2=py27_0">numpy</requirement> 5 <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
6 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> 6 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
63 <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"> 63 <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">
64 <option value="indexed">Use a built-in index</option> 64 <option value="indexed">Use a built-in index</option>
65 <option value="history">Use one from the history</option> 65 <option value="history">Use one from the history</option>
66 </param> 66 </param>
67 <when value="indexed"> 67 <when value="indexed">
68 <repeat name="series" title="Add alignment files"> 68 <repeat name="series" title="Add alignment files" min="1">
69 <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"> 69 <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam">
70 <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."/> 70 <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."/>
71 </param> 71 </param>
72 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/> 72 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
73 </repeat> 73 </repeat>
74 </when> 74 </when>
75 <when value="history"> 75 <when value="history">
76 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, that served as the reference index for the alignments" /> 76 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, that served as the reference index for the alignments" />
77 <repeat name="series" title="Add alignment files"> 77 <repeat name="series" title="Add alignment files" min="1">
78 <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"/> 78 <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"/>
79 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/> 79 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
80 </repeat> 80 </repeat>
81 </when> 81 </when>
82 </conditional> 82 </conditional>