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comparison pretext_map.xml @ 5:287782c826b2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 2743362d5b18e0972fafba54acc522be69a05c61"
author iuc
date Fri, 19 Nov 2021 23:19:30 +0000
parents 8e8d97a13895
children 1ae5b58fe3e6
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4:8e8d97a13895 5:287782c826b2
1 <tool id="pretext_map" name="PretextMap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> 1 <tool id="pretext_map" name="PretextMap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>converts SAM or BAM files into genome contact maps</description> 2 <description>converts SAM or BAM files into genome contact maps</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">0.1.8</token> 4 <token name="@TOOL_VERSION@">0.1.8</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">2</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">pretextmap</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">pretextmap</requirement>
9 <requirement type="package" version="1.13">samtools</requirement> 9 <requirement type="package" version="1.13">samtools</requirement>
10 </requirements> 10 </requirements>
43 </param> 43 </param>
44 <when value="nosort"/> 44 <when value="nosort"/>
45 <when value="length"> 45 <when value="length">
46 <param argument="--sortorder" type="select" label="Sort order: "> 46 <param argument="--sortorder" type="select" label="Sort order: ">
47 <option value="ascend">Ascending</option> 47 <option value="ascend">Ascending</option>
48 <option value="decend">Decending</option> 48 <option value="descend">Descending</option>
49 </param> 49 </param>
50 </when> 50 </when>
51 <when value="name"> 51 <when value="name">
52 <param argument="--sortorder" type="select" label="Sort order: "> 52 <param argument="--sortorder" type="select" label="Sort order: ">
53 <option value="ascend">Ascending</option> 53 <option value="ascend">Ascending</option>
54 <option value="descend">Decending</option> 54 <option value="descend">Descending</option>
55 </param> 55 </param>
56 </when> 56 </when>
57 </conditional> 57 </conditional>
58 <param name="map_qual" argument="--mapq" type="integer" label="Minimum mapping quality:" min="0" value="10" optional="true" help=" Filter mapped read by minimum MAPQ. Useful to remove spurious contacts from multimapping reads"/> 58 <param name="map_qual" argument="--mapq" type="integer" label="Minimum mapping quality:" min="0" value="10" optional="true" help=" Filter mapped read by minimum MAPQ. Useful to remove spurious contacts from multimapping reads"/>
59 <conditional name="filter"> 59 <conditional name="filter">