Mercurial > repos > iuc > crossmap_wig

changeset 9:f7229c8445da draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
author iuc
date Mon, 02 Sep 2024 12:01:52 +0000
parents e72c320c17c1
children
files crossmap_wig.xml macros.xml
diffstat 2 files changed, 10 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/crossmap_wig.xml	Thu Jan 20 04:30:30 2022 +0000
+++ b/crossmap_wig.xml	Mon Sep 02 12:01:52 2024 +0000
@@ -7,38 +7,32 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-CrossMap.py wig
+CrossMap wig
 '${chain_source.input_chain}'
 '${input}'
 output
     ]]></command>
-
     <inputs>
         <param name="input" type="data" format="wig" label="Wiggle file"/>
-
-        <expand macro="chain" />
+        <expand macro="chain"/>
     </inputs>
-
     <outputs>
-        <data name="output" format="bigwig" label="${tool.name} on ${on_string}" from_work_dir="output.bw" />
-        <data name="output2" format="bedgraph" label="${tool.name} (bedgraph) on ${on_string}" from_work_dir="output.sorted.bgr" />
+        <data name="output" format="bigwig" label="${tool.name} on ${on_string}" from_work_dir="output.bw"/>
+        <data name="output2" format="bedgraph" label="${tool.name} (bedgraph) on ${on_string}" from_work_dir="output.sorted.bgr"/>
     </outputs>
-
     <tests>
-    <!-- WIG - Doesn't understand fixedStep -->
+        <!-- WIG - Doesn't understand fixedStep -->
         <test>
             <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/>
             <param name="index_source" value="history"/>
             <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
-
             <output name="output" file="test_wig_01_output_a.bw"/>
             <output name="output2" file="test_wig_01_output_a.sorted.bgr"/>
         </test>
-
-        <test><!-- cached reference genome -->
-            <param name="input" value="test_wig_01_input_a.wig" ftype="wig" dbkey="hg18" />
+        <test>
+            <!-- cached reference genome -->
+            <param name="input" value="test_wig_01_input_a.wig" ftype="wig" dbkey="hg18"/>
             <param name="index_source" value="cached"/>
-
             <output name="output" file="test_wig_01_output_a.bw"/>
             <output name="output2" file="test_wig_01_output_a.sorted.bgr"/>
         </test>
@@ -57,7 +51,6 @@
 smaller than file in wiggle format, and more importantly, CrossMap
 internally transforms wiggle into bedGraph to increase running speed.
     ]]></help>
-
     <citations>
         <citation type="doi">10.1093/bioinformatics/btt730</citation>
     </citations>
--- a/macros.xml	Thu Jan 20 04:30:30 2022 +0000
+++ b/macros.xml	Mon Sep 02 12:01:52 2024 +0000
@@ -1,4 +1,3 @@
-<?xml version="1.0"?>
 <macros>
     <xml name="requirements">
         <requirements>
@@ -6,7 +5,7 @@
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">0.6.1</token>
+    <token name="@TOOL_VERSION@">0.7.0</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="stdio">
         <stdio>
@@ -17,7 +16,7 @@
     </xml>
     <xml name="version_command">
         <version_command><![CDATA[
-CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'
+CrossMap 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'
         ]]></version_command>
     </xml>
     <xml name="chain">