| Previous changeset 3:d256a51a656b (2021-09-13) Next changeset 5:2b16ba799da9 (2021-11-19) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 21b72bf355117b1b6cf0fb13fa34139395409011" |
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modified:
pretext_map.xml |
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| diff -r d256a51a656b -r bbe19ef04a74 pretext_map.xml --- a/pretext_map.xml Mon Sep 13 10:49:00 2021 +0000 +++ b/pretext_map.xml Thu Nov 11 15:05:34 2021 +0000 |
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| @@ -1,7 +1,8 @@ <tool id="pretext_map" name="PretextMap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> + <description>converts SAM or BAM files into genome contact maps</description> <macros> <token name="@TOOL_VERSION@">0.1.8</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">pretextmap</requirement> @@ -35,9 +36,9 @@ <inputs> <param name="input" type="data" format="sam,bam" label="Input dataset in SAM or BAM format"/> <conditional name="sorting"> - <param argument="--sortby" type="select" label="Sort by"> - <option value="nosort" selected="true">Don't sort</option> - <option value="length">Length</option> + <param argument="--sortby" type="select" label="Sort by" help="Sort the genome by length or name of the scaffolds"> + <option value="nosort">Don't sort</option> + <option value="length" selected="true">Length</option> <option value="name">Name</option> </param> <when value="nosort"/> @@ -54,9 +55,9 @@ </param> </when> </conditional> - <param name="map_qual" type="integer" label="Minimum mapping quality:" min="0" optional="true"/> + <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"/> <conditional name="filter"> - <param name="filter_type" type="select" label="How to filter: "> + <param name="filter_type" type="select" label="How to filter: " help="Subset the output excluding a list of scaffolds"> <option value="" selected="true">No filter</option> <option value="in">Filter to include only specified sequence names</option> <option value="out">Filter to exclude specified sequence names</option> @@ -118,9 +119,7 @@ **What is does** -The Paired REad TEXTure Mapper converts aligned read pairs into genome contact maps. -Pretext has no special requirement on the alignment files -process your alignments however you want before feeding to PretextMap. +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>`_. ]]></help> <citations> |