Mercurial > repos > iuc > pretext_map

comparison pretext_map.xml @ 4:bbe19ef04a74 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 21b72bf355117b1b6cf0fb13fa34139395409011"
author iuc
date Thu, 11 Nov 2021 15:05:34 +0000
parents d256a51a656b
children 2b16ba799da9
comparison
equal deleted inserted replaced
3:d256a51a656b 4:bbe19ef04a74
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 <macros> 3 <macros>
3 <token name="@TOOL_VERSION@">0.1.8</token> 4 <token name="@TOOL_VERSION@">0.1.8</token>
4 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
5 </macros> 6 </macros>
6 <requirements> 7 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">pretextmap</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">pretextmap</requirement>
8 <requirement type="package" version="1.13">samtools</requirement> 9 <requirement type="package" version="1.13">samtools</requirement>
9 </requirements> 10 </requirements>
33 -o output.pretext 34 -o output.pretext
34 ]]></command> 35 ]]></command>
35 <inputs> 36 <inputs>
36 <param name="input" type="data" format="sam,bam" label="Input dataset in SAM or BAM format"/> 37 <param name="input" type="data" format="sam,bam" label="Input dataset in SAM or BAM format"/>
37 <conditional name="sorting"> 38 <conditional name="sorting">
38 <param argument="--sortby" type="select" label="Sort by"> 39 <param argument="--sortby" type="select" label="Sort by" help="Sort the genome by length or name of the scaffolds">
39 <option value="nosort" selected="true">Don't sort</option> 40 <option value="nosort">Don't sort</option>
40 <option value="length">Length</option> 41 <option value="length" selected="true">Length</option>
41 <option value="name">Name</option> 42 <option value="name">Name</option>
42 </param> 43 </param>
43 <when value="nosort"/> 44 <when value="nosort"/>
44 <when value="length"> 45 <when value="length">
45 <param argument="--sortorder" type="select" label="Sort order: "> 46 <param argument="--sortorder" type="select" label="Sort order: ">
52 <option value="ascend">Ascending</option> 53 <option value="ascend">Ascending</option>
53 <option value="descend">Decending</option> 54 <option value="descend">Decending</option>
54 </param> 55 </param>
55 </when> 56 </when>
56 </conditional> 57 </conditional>
57 <param name="map_qual" type="integer" label="Minimum mapping quality:" min="0" optional="true"/> 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 <conditional name="filter"> 59 <conditional name="filter">
59 <param name="filter_type" type="select" label="How to filter: "> 60 <param name="filter_type" type="select" label="How to filter: " help="Subset the output excluding a list of scaffolds">
60 <option value="" selected="true">No filter</option> 61 <option value="" selected="true">No filter</option>
61 <option value="in">Filter to include only specified sequence names</option> 62 <option value="in">Filter to include only specified sequence names</option>
62 <option value="out">Filter to exclude specified sequence names</option> 63 <option value="out">Filter to exclude specified sequence names</option>
63 </param> 64 </param>
64 <when value=""/> 65 <when value=""/>
116 </tests> 117 </tests>
117 <help><![CDATA[ 118 <help><![CDATA[
118 119
119 **What is does** 120 **What is does**
120 121
121 The Paired REad TEXTure Mapper converts aligned read pairs into genome contact maps. 122 PretextMap (Paired REad TEXTure Mapper) converts SAM/BAM/CRAM or `pairs files <https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md>`_ into `genome contact maps <https://genome.ucsc.edu/goldenPath/help/hic.html>`_.
122 Pretext has no special requirement on the alignment files
123 process your alignments however you want before feeding to PretextMap.
124 123
125 ]]></help> 124 ]]></help>
126 <citations> 125 <citations>
127 <citation type="bibtex"> 126 <citation type="bibtex">
128 @misc{Harry_et_al, 127 @misc{Harry_et_al,