# HG changeset patch
# User iuc
# Date 1636643050 0
# Node ID 8e8d97a138954cb835c75947009b2e1df18805d7
# Parent  94176d166ff21fa5177acea53c2b2e38e7d62814
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 21b72bf355117b1b6cf0fb13fa34139395409011"

diff -r 94176d166ff2 -r 8e8d97a13895 pretext_map.xml
--- a/pretext_map.xml	Mon Sep 13 10:47:38 2021 +0000
+++ b/pretext_map.xml	Thu Nov 11 15:04:10 2021 +0000
@@ -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>