Mercurial > repos > iuc > circos

changeset 11:31a35811dda6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit b9ec351920dbc83fa14bd1f8cfdd0a6a19b89473"
author iuc
date Tue, 16 Nov 2021 09:20:08 +0000
parents 7f13dc906cb9
children 290a11559985
files alignments-to-links.xml bundlelinks.xml circos.xml gc_skew.xml macros.xml resample.xml scatter-from-wiggle.xml stack-histogram.xml text-from-interval.xml tiles-from-interval.xml
diffstat 10 files changed, 14 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/alignments-to-links.xml	Mon Oct 11 10:09:51 2021 +0000
+++ b/alignments-to-links.xml	Tue Nov 16 09:20:08 2021 +0000
@@ -4,8 +4,6 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-    </expand>
     <edam_topics>
         <edam_topic>topic_0797</edam_topic>
         <edam_topic>topic_0092</edam_topic>
@@ -13,6 +11,8 @@
     <edam_operations>
         <edam_operation>operation_1812</edam_operation>
     </edam_operations>
+    <expand macro="requirements">
+    </expand>
     <command detect_errors="exit_code"><![CDATA[
 python '$__tool_directory__/alignments-to-links.py' '$input' '$input.ext' > '$output'
     ]]></command>
--- a/bundlelinks.xml	Mon Oct 11 10:09:51 2021 +0000
+++ b/bundlelinks.xml	Tue Nov 16 09:20:08 2021 +0000
@@ -4,7 +4,6 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <edam_topics>
         <edam_topic>topic_0797</edam_topic>
         <edam_topic>topic_0092</edam_topic>
@@ -12,6 +11,7 @@
     <edam_operations>
         <edam_operation>operation_3436</edam_operation>
     </edam_operations>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 bundlelinks
     #if $max_gap:
--- a/circos.xml	Mon Oct 11 10:09:51 2021 +0000
+++ b/circos.xml	Tue Nov 16 09:20:08 2021 +0000
@@ -11,7 +11,6 @@
         <import>macros_conffiles.xml</import>
         <import>macros_tests.xml</import>
     </macros>
-    <expand macro="requirements"/>
     <edam_topics>
         <edam_topic>topic_0797</edam_topic>
         <edam_topic>topic_0092</edam_topic>
@@ -19,7 +18,7 @@
     <edam_operations>
         <edam_operation>operation_0337</edam_operation>
     </edam_operations>
-    <version_command>circos --version</version_command>
+    <expand macro="requirements"/>
     <stdio>
       <!-- Anything other than zero is an error -->
       <exit_code range="1:"/>
@@ -27,6 +26,7 @@
       <!-- In case the return code has not been set propery check stderr too -->
       <regex match="Circos::Error::fatal_error.* called at"/>
     </stdio>
+    <version_command>circos --version</version_command>
     <command><![CDATA[
 ## Directory structure
 mkdir -p circos/conf/ circos/data/ &&
@@ -58,7 +58,7 @@
         genomeref.fa
         > circos/conf/karyotype.txt &&
 #else if $reference_genome.ref.ref_source == 'preset':
-    cp '$__tool_directory__/karyotype/'${reference_genome.ref.preset_karyotype} circos/conf/karyotype.txt &&
+    cp '$__tool_directory__/karyotype/${reference_genome.ref.preset_karyotype}' circos/conf/karyotype.txt &&
 #end if
 
 python '$__tool_directory__/karyotype-colors.py' `grep -c '^chr\s' 'circos/conf/karyotype.txt'`
--- a/gc_skew.xml	Mon Oct 11 10:09:51 2021 +0000
+++ b/gc_skew.xml	Tue Nov 16 09:20:08 2021 +0000
@@ -4,8 +4,6 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-    </expand>
     <edam_topics>
         <edam_topic>topic_0797</edam_topic>
         <edam_topic>topic_0092</edam_topic>
@@ -13,6 +11,8 @@
     <edam_operations>
         <edam_operation>operation_0262</edam_operation>
     </edam_operations>
+    <expand macro="requirements">
+    </expand>
     <command detect_errors="exit_code"><![CDATA[
 ln -s -f
 #if $reference_genome.reference_genome_source == "history"
--- a/macros.xml	Mon Oct 11 10:09:51 2021 +0000
+++ b/macros.xml	Tue Nov 16 09:20:08 2021 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
   <token name="@TOOL_VERSION@">0.69.8</token>
-  <token name="@VERSION_SUFFIX@">8</token>
+  <token name="@VERSION_SUFFIX@">9</token>
 
   <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy@VERSION_SUFFIX@</token>
 
--- a/resample.xml	Mon Oct 11 10:09:51 2021 +0000
+++ b/resample.xml	Tue Nov 16 09:20:08 2021 +0000
@@ -4,7 +4,6 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <edam_topics>
         <edam_topic>topic_0797</edam_topic>
         <edam_topic>topic_0092</edam_topic>
@@ -12,6 +11,7 @@
     <edam_operations>
         <edam_operation>operation_3436</edam_operation>
     </edam_operations>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 resample
     -bin '$bins'
--- a/scatter-from-wiggle.xml	Mon Oct 11 10:09:51 2021 +0000
+++ b/scatter-from-wiggle.xml	Tue Nov 16 09:20:08 2021 +0000
@@ -4,8 +4,6 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-    </expand>
     <edam_topics>
         <edam_topic>topic_0797</edam_topic>
         <edam_topic>topic_0092</edam_topic>
@@ -13,6 +11,7 @@
     <edam_operations>
         <edam_operation>operation_3434</edam_operation>
     </edam_operations>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 python '$__tool_directory__/scatter-from-wiggle.py' '$input' > '$output'
     ]]></command>
--- a/stack-histogram.xml	Mon Oct 11 10:09:51 2021 +0000
+++ b/stack-histogram.xml	Tue Nov 16 09:20:08 2021 +0000
@@ -4,8 +4,6 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-    </expand>
     <edam_topics>
         <edam_topic>topic_0797</edam_topic>
         <edam_topic>topic_0092</edam_topic>
@@ -13,6 +11,7 @@
     <edam_operations>
         <edam_operation>operation_0335</edam_operation>
     </edam_operations>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 python
     '$__tool_directory__/stack-histogram.py'
--- a/text-from-interval.xml	Mon Oct 11 10:09:51 2021 +0000
+++ b/text-from-interval.xml	Tue Nov 16 09:20:08 2021 +0000
@@ -4,8 +4,6 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-    </expand>
     <edam_topics>
         <edam_topic>topic_0797</edam_topic>
         <edam_topic>topic_0092</edam_topic>
@@ -13,6 +11,7 @@
     <edam_operations>
         <edam_operation>operation_3434</edam_operation>
     </edam_operations>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 python
 #if $ref.ref_source == 'gff3':
--- a/tiles-from-interval.xml	Mon Oct 11 10:09:51 2021 +0000
+++ b/tiles-from-interval.xml	Tue Nov 16 09:20:08 2021 +0000
@@ -4,8 +4,6 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-    </expand>
     <edam_topics>
         <edam_topic>topic_0797</edam_topic>
         <edam_topic>topic_0092</edam_topic>
@@ -13,6 +11,7 @@
     <edam_operations>
         <edam_operation>operation_3434</edam_operation>
     </edam_operations>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 python
 #if $ref.ref_source == 'gff3':