Mercurial > repos > iuc > proteinortho_grab_proteins

changeset 1:fa2d1e652ec1 draft

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"planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
author iuc
date Tue, 14 Sep 2021 11:39:49 +0000
parents d348c3a151d9
children 85ffb2cc6b64
files proteinortho_grab_proteins.xml proteinortho_macros.xml
diffstat 2 files changed, 14 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/proteinortho_grab_proteins.xml	Tue Feb 18 17:57:53 2020 -0500
+++ b/proteinortho_grab_proteins.xml	Tue Sep 14 11:39:49 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="proteinortho_grab_proteins" name="Proteinortho grab proteins" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@">
+<tool id="proteinortho_grab_proteins" name="Proteinortho grab proteins" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" profile="@PROFLE@">
     <description>finds genes/proteins in a given fasta file</description>
     <macros>
         <import>proteinortho_macros.xml</import>
@@ -53,6 +53,10 @@
                             <add value="\\"/>
                             <add value="_"/>
                             <add value="|"/>
+                            <add value="\t"/>
+                            <add value="&#9;"/> <!-- tab -->
+                            <add value=","/>
+                            <add value=";"/>
                             <add value="&#91;"/> <!-- left square bracket, e.g subselecting from vec[1] -->
                             <add value="&#93;"/> <!-- right square bracket -->
                             <add value="&#40;"/> <!-- left parenthesis -->
--- a/proteinortho_macros.xml	Tue Feb 18 17:57:53 2020 -0500
+++ b/proteinortho_macros.xml	Tue Sep 14 11:39:49 2021 +0000
@@ -1,7 +1,8 @@
 <?xml version="1.0"?>
 <macros>
-   <token name="@TOOL_VERSION@">6.0.14</token>
-   <token name="@WRAPPER_VERSION@">2.9.1</token>
+   <token name="@TOOL_VERSION@">6.0.31</token>
+   <token name="@WRAPPER_VERSION@">0</token>
+   <token name="@PROFILE@">20.09</token>
    <xml name="citations">
         <citations>
             <citation type="doi">10.1186/1471-2105-12-124</citation>
@@ -11,10 +12,12 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">proteinortho</requirement>
-            <requirement type="package">diamond</requirement>
-            <requirement type="package">blast</requirement>
-            <requirement type="package">blat</requirement>
-            <requirement type="package">last</requirement>
+            <!-- blast, blat, and last are not in the biopython requirements
+                 diamond is, but latest version does not work: https://gitlab.com/paulklemm_PHD/proteinortho/-/issues/55 -->
+            <requirement type="package" version="2.0.9">diamond</requirement>
+            <requirement type="package" version="2.12.0">blast</requirement>
+            <requirement type="package" version="36">blat</requirement>
+            <requirement type="package" version="1256">last</requirement>
         </requirements>
     </xml>
     <xml name="version_command">