Mercurial > repos > dfornika > mentalist

changeset 67:03c37b300f43 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit d6aa0144475c93626400a46e933acbbd77fefb01-dirty
author dfornika
date Fri, 15 Jun 2018 16:37:07 -0400
parents 9027f18a23f4
children e26b21ebf828
files data_managers/data_manager_conf.xml data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml tools/mentalist_call/mentalist_call.xml tools/mentalist_distance/mentalist_distance.xml tools/mentalist_tree/mentalist_tree.xml
diffstat 8 files changed, 18 insertions(+), 22 deletions(-) [+]
line wrap: on
line diff
--- a/data_managers/data_manager_conf.xml	Thu Jun 14 16:29:59 2018 -0400
+++ b/data_managers/data_manager_conf.xml	Fri Jun 15 16:37:07 2018 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <data_managers>
-  <data_manager tool_file="data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml" id="mentalist_build_db" version="0.1.8">
+  <data_manager tool_file="data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml" id="mentalist_build_db" version="0.1.9">
     <data_table name="mentalist_databases">
       <output>
         <column name="value" />
@@ -15,7 +15,7 @@
       </output>
     </data_table>
   </data_manager>
-  <data_manager tool_file="data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml" id="mentalist_download_cgmlst" version="0.1.8">
+  <data_manager tool_file="data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml" id="mentalist_download_cgmlst" version="0.1.9">
     <data_table name="mentalist_databases">
       <output>
         <column name="value" />
@@ -30,7 +30,7 @@
       </output>
     </data_table>
   </data_manager>
-  <data_manager tool_file="data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml" id="mentalist_download_pubmlst" version="0.1.8">
+  <data_manager tool_file="data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml" id="mentalist_download_pubmlst" version="0.1.9">
     <data_table name="mentalist_databases">
       <output>
         <column name="value" />
@@ -45,7 +45,7 @@
       </output>
     </data_table>
   </data_manager>
-  <data_manager tool_file="data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml" id="mentalist_download_enterobase" version="0.1.8">
+  <data_manager tool_file="data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml" id="mentalist_download_enterobase" version="0.1.9">
     <data_table name="mentalist_databases">
       <output>
         <column name="value" />
--- a/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml	Thu Jun 14 16:29:59 2018 -0400
+++ b/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml	Fri Jun 15 16:37:07 2018 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="0.1.8">
+<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="0.1.9">
   <requirements>
-    <requirement type="package" version="0.1.8">mentalist</requirement>
+    <requirement type="package" version="0.1.9">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
   <![CDATA[
--- a/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml	Thu Jun 14 16:29:59 2018 -0400
+++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml	Fri Jun 15 16:37:07 2018 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="mentalist_download_cgmlst" name="MentaLiST Download from cgMLST" tool_type="manage_data" version="0.1.8">
+<tool id="mentalist_download_cgmlst" name="MentaLiST Download from cgMLST" tool_type="manage_data" version="0.1.9">
   <requirements>
-    <requirement type="package" version="0.1.8">mentalist</requirement>
+    <requirement type="package" version="0.1.9">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
--- a/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml	Thu Jun 14 16:29:59 2018 -0400
+++ b/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml	Fri Jun 15 16:37:07 2018 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="mentalist_download_enterobase" name="MentaLiST Download from Enterobase" tool_type="manage_data" version="0.1.8">
+<tool id="mentalist_download_enterobase" name="MentaLiST Download from Enterobase" tool_type="manage_data" version="0.1.9">
   <requirements>
-    <requirement type="package" version="0.1.8">mentalist</requirement>
+    <requirement type="package" version="0.1.9">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
--- a/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml	Thu Jun 14 16:29:59 2018 -0400
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml	Fri Jun 15 16:37:07 2018 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="mentalist_download_pubmlst" name="MentaLiST Download from pubMLST" tool_type="manage_data" version="0.1.8">
+<tool id="mentalist_download_pubmlst" name="MentaLiST Download from pubMLST" tool_type="manage_data" version="0.1.9">
   <requirements>
-    <requirement type="package" version="0.1.8">mentalist</requirement>
+    <requirement type="package" version="0.1.9">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
--- a/tools/mentalist_call/mentalist_call.xml	Thu Jun 14 16:29:59 2018 -0400
+++ b/tools/mentalist_call/mentalist_call.xml	Fri Jun 15 16:37:07 2018 -0400
@@ -1,6 +1,6 @@
-<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.8">
+<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.9">
   <requirements>
-    <requirement type="package" version="0.1.8">mentalist</requirement>
+    <requirement type="package" version="0.1.9">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
     mentalist
--- a/tools/mentalist_distance/mentalist_distance.xml	Thu Jun 14 16:29:59 2018 -0400
+++ b/tools/mentalist_distance/mentalist_distance.xml	Fri Jun 15 16:37:07 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="mentalist_distance" name="MentaLiST Distance Matrix" version="0.1.8">
+<tool id="mentalist_distance" name="MentaLiST Distance Matrix" version="0.1.9">
   <requirements>
     <requirement type="package" version="3.4.1">r-base</requirement>
   </requirements>
--- a/tools/mentalist_tree/mentalist_tree.xml	Thu Jun 14 16:29:59 2018 -0400
+++ b/tools/mentalist_tree/mentalist_tree.xml	Fri Jun 15 16:37:07 2018 -0400
@@ -1,6 +1,6 @@
-<tool id="mentalist_tree" name="MentaLiST Tree" version="0.1.8">
+<tool id="mentalist_tree" name="MentaLiST Tree" version="0.1.9">
   <requirements>
-    <requirement type="package" version="1.70">biopython</requirement>
+    <requirement type="package" version="1.71">biopython</requirement>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
     $__tool_directory__/mentalist_tree
@@ -20,11 +20,7 @@
     </test>
     <test>
       <param name="input" value="mentalist_tree/med_input_00.tsv" />
-      <output name="output" file="mentalits_tree/med_output_00.nwk" />
-    </test>
-    <test>
-      <param name="input" value="mentalist_tree/large_input_00.tsv" />
-      <output name="output" file="mentalist_tree/large_output_00.nwk" />
+      <output name="output" file="mentalitst_tree/med_output_00.nwk" />
     </test>
   </tests>
   <help><![CDATA[