Mercurial > repos > petr-novak > various_galaxy_tools

changeset 2:90c46e40d222 draft

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planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 248ffeb6792d5807820b664eae3e88306f3f395e-dirty
author petr-novak
date Mon, 26 Feb 2024 13:11:53 +0000
parents 639c0edb7e64
children 1069776f7ae2
files extract_GFF_Features.xml gff2bed.xml gff2tabular.xml gff_filter_by_attribute.xml
diffstat 4 files changed, 13 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/extract_GFF_Features.xml	Mon Feb 26 12:59:20 2024 +0000
+++ b/extract_GFF_Features.xml	Mon Feb 26 13:11:53 2024 +0000
@@ -1,5 +1,8 @@
 <tool id="Extract_features1" name="Extract features" version="1.0.0">
   <description>from GFF data</description>
+  <required_files>
+    <include type="literal" path="extract_GFF_Features.py"/>
+  </required_files>
   <command>
     python '$__tool_directory__'/extract_GFF_Features.py $input1 $out_file1 ${column_choice.col} ${column_choice.feature}</command>
   <inputs>
--- a/gff2bed.xml	Mon Feb 26 12:59:20 2024 +0000
+++ b/gff2bed.xml	Mon Feb 26 13:11:53 2024 +0000
@@ -1,8 +1,11 @@
 <tool id="gff2bed1" name="GFF-to-BED" version="1.0.2">
   <description>converter</description>
   <edam_operations>
-    <edam_operation>operation_3434</edam_operation>
+  <edam_operation>operation_3434</edam_operation>
   </edam_operations>
+  <required_files>
+    <include type="literal" path="gff_to_bed_converter.py"/>
+  </required_files>
   <command>
       python '$__tool_directory__'/gff_to_bed_converter.py $input $out_file1
   </command>
--- a/gff2tabular.xml	Mon Feb 26 12:59:20 2024 +0000
+++ b/gff2tabular.xml	Mon Feb 26 13:11:53 2024 +0000
@@ -4,6 +4,9 @@
         <requirement type="package">R</requirement>
         <requirement type="package">bioconductor-rtracklayer</requirement>
     </requirements>
+    <required_files>
+        <include type="literal" path="gff2tabular.R"/>
+    </required_files>
     <command detect_errors="exit_code"><![CDATA[
         Rscript ${__tool_directory__}/gff2tabular.R '$inputgff' '$output'
     ]]></command>
--- a/gff_filter_by_attribute.xml	Mon Feb 26 12:59:20 2024 +0000
+++ b/gff_filter_by_attribute.xml	Mon Feb 26 13:11:53 2024 +0000
@@ -1,5 +1,8 @@
 <tool id="gff_filter_by_attribute" name="Filter GFF data by attribute" version="0.2">
   <description>using simple expressions</description>
+    <required_files>
+        <include type="literal" path="gff_filter_by_attribute.py"/>
+</required_files>
   <command>
 python '$__tool_directory__/gff_filter_by_attribute.py' '$input' '$out_file1' '$cond' '${input.metadata.attribute_types}'
   </command>