Mercurial > repos > drosofff > msp_sr_size_histograms

comparison size_histogram.xml @ 4:f0b489448615 draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Mon, 29 Jun 2015 05:56:53 -0400
parents afe1e306e2a8
children 27c1327f5687
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3:afe1e306e2a8 4:f0b489448615
1 <tool id="Size_histogram" name="Generate size histograms from alignment files" version="0.9.6"> 1 <tool id="Size_histogram" name="Generate size histograms from alignment files" version="0.9.6">
2 <description>from sRbowtie aligment</description> 2 <description>from sRbowtie aligment</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="0.1.18">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="2.14">biocbasics</requirement> 6 <requirement type="package" version="2.14">biocbasics</requirement>
8 <requirement type="package" version="1.9">numpy</requirement> 7 <requirement type="package" version="1.9">numpy</requirement>
9 </requirements> 8 </requirements>
10 <command interpreter="python"> 9 <command interpreter="python">
59 <option value="indexed">Use a built-in index</option> 58 <option value="indexed">Use a built-in index</option>
60 <option value="history">Use one from the history</option> 59 <option value="history">Use one from the history</option>
61 </param> 60 </param>
62 <when value="indexed"> 61 <when value="indexed">
63 <repeat name="series" title="Add alignment files"> 62 <repeat name="series" title="Add alignment files">
64 <param name="input" type="data" label="Select multiple alignments to parse"> 63 <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam">
65 <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."/> 64 <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."/>
66 </param> 65 </param>
67 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/> 66 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
68 </repeat> 67 </repeat>
69 </when> 68 </when>
70 <when value="history"> 69 <when value="history">
71 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" /> 70 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
72 <repeat name="series" title="Add alignment files"> 71 <repeat name="series" title="Add alignment files">
73 <param name="input" type="data" label="Select multiple alignments to parse"/> 72 <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"/>
74 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/> 73 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
75 </repeat> 74 </repeat>
76 </when> 75 </when>
77 </conditional> 76 </conditional>
78 <param name="gff" type="data" optional="true" label="Optional: select a GFF to investigate regions of interest" help="GFF must match genome build"/> 77 <param name="gff" type="data" format="gff,gff3" optional="true" label="Optional: select a GFF to investigate regions of interest" help="GFF must match genome build"/>
79 <!-- <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="GFF database and alignment file databse do not match!"/> --> 78 <!-- <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="GFF database and alignment file databse do not match!"/> -->
80 <param name="global" type="select" label="Generate size distribution for each item, or generate a global alignment"> 79 <param name="global" type="select" label="Generate size distribution for each item, or generate a global alignment">
81 <option value="no">for each item</option> 80 <option value="no">for each item</option>
82 <option value="yes">global</option> 81 <option value="yes">global</option>
83 </param> 82 </param>