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comparison pretext_map.xml @ 10:be286033206a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext commit 9cf789f5e40015218bd898732ead767a3b897c6a
author iuc
date Tue, 24 Feb 2026 09:59:30 +0000
parents b070f46b218c
children
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9:439f16020bb0 10:be286033206a
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@">0.1.9</token> 4 <token name="@TOOL_VERSION@">0.2.3</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">0</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="1.14">samtools</requirement> 9 <requirement type="package" version="1.14">samtools</requirement>
10 </requirements> 10 </requirements>
29 #if $filter.filter_type == "in": 29 #if $filter.filter_type == "in":
30 --filterInclude '$filter.filter_list' 30 --filterInclude '$filter.filter_list'
31 #elif $filter.filter_type == "out": 31 #elif $filter.filter_type == "out":
32 --filterExclude '$filter.filter_list' 32 --filterExclude '$filter.filter_list'
33 #end if 33 #end if
34 $highRes
34 -o output.pretext 35 -o output.pretext
35 ]]></command> 36 ]]></command>
36 <inputs> 37 <inputs>
37 <param name="input" type="data" format="sam,bam" label="Input dataset in SAM or BAM format"/> 38 <param name="input" type="data" format="sam,bam" label="Input dataset in SAM or BAM format"/>
39 <param argument="--highRes" type="boolean" truevalue="--highRes" falsevalue="" label="High resolution mode" help="Use high resolution mode for better contact map resolution"/>
38 <conditional name="sorting"> 40 <conditional name="sorting">
39 <param argument="--sortby" type="select" label="Sort by" help="Sort the genome by length or name of the scaffolds"> 41 <param argument="--sortby" type="select" label="Sort by" help="Sort the genome by length or name of the scaffolds">
40 <option value="nosort">Don't sort</option> 42 <option value="nosort">Don't sort</option>
41 <option value="length" selected="true">Length</option> 43 <option value="length" selected="true">Length</option>
42 <option value="name">Name</option> 44 <option value="name">Name</option>
89 <data format="pretext" name="pretext_map_out" from_work_dir="output.pretext" label="${tool.name} on ${on_string}"/> 91 <data format="pretext" name="pretext_map_out" from_work_dir="output.pretext" label="${tool.name} on ${on_string}"/>
90 </outputs> 92 </outputs>
91 <tests> 93 <tests>
92 <test> 94 <test>
93 <param name="input" ftype="bam" value="test.bam"/> 95 <param name="input" ftype="bam" value="test.bam"/>
96 <param name="highRes" value="true"/>
94 <conditional name="sorting"> 97 <conditional name="sorting">
95 <param name="sortby" value="length"/> 98 <param name="sortby" value="length"/>
96 <param name="sortorder" value="ascend"/> 99 <param name="sortorder" value="ascend"/>
97 </conditional> 100 </conditional>
98 <conditional name="filter"> 101 <conditional name="filter">
99 <param name="filter_type" value="in"/> 102 <param name="filter_type" value="in"/>
100 <param name="filter_list" value="ref"/> 103 <param name="filter_list" value="ref"/>
101 </conditional> 104 </conditional>
102 <param name="map_qual" value="10"/> 105 <param name="map_qual" value="10"/>
103 <output name="pretext_map_out" file="output_1.pretext"/> 106 <output name="pretext_map_out">
107 <assert_contents>
108 <has_size value="2225023" delta="1000"/>
109 </assert_contents>
110 </output>
104 </test> 111 </test>
105 <test> 112 <test>
106 <param name="input" ftype="sam" value="test.sam"/> 113 <param name="input" ftype="sam" value="test.sam"/>
114 <param name="highRes" value="false"/>
107 <conditional name="sorting"> 115 <conditional name="sorting">
108 <param name="sortby" value="name"/> 116 <param name="sortby" value="name"/>
109 <param name="sortorder" value="descend"/> 117 <param name="sortorder" value="descend"/>
110 </conditional> 118 </conditional>
111 <conditional name="filter"> 119 <conditional name="filter">