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changeset 6:19c265784f35 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 88d7f81768f05f490f444b646f47241cf2547b44"
author iuc
date Sat, 27 Nov 2021 10:12:45 +0000
parents f5a5a2b39ff2
children eca7ac1eb423
files lastal.xml lastdb.xml lastsplit.xml lasttrain.xml macros_last.xml maf-convert.xml
diffstat 6 files changed, 22 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/lastal.xml	Thu Mar 25 20:53:27 2021 +0000
+++ b/lastal.xml	Sat Nov 27 10:12:45 2021 +0000
@@ -1,13 +1,13 @@
-<tool id="last_al" name="LASTal" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01">
+<tool id="last_al" name="LASTal" version="@TOOL_VERSION@+galaxy1" profile="20.01">
 
     <description>finds local alignments between query sequences, and reference sequences.</description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros_last.xml</import>
     </macros>
 
     <requirements>
-        <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">last</requirement>
     </requirements>
 
     <command detect_errors="exit_code"><![CDATA[
@@ -77,6 +77,7 @@
         -w $lastal.misc_opt.w
         -u $lastal.misc_opt.u
         -g $lastal.misc_opt.g
+        -G $lastal.misc_opt.G
 
         -P \${GALAXY_SLOTS:-1}
 
--- a/lastdb.xml	Thu Mar 25 20:53:27 2021 +0000
+++ b/lastdb.xml	Sat Nov 27 10:12:45 2021 +0000
@@ -1,13 +1,13 @@
-<tool id="last_db" name="LASTdb" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01">
+<tool id="last_db" name="LASTdb" version="@TOOL_VERSION@+galaxy0" profile="20.01">
 
     <description>prepares sequences for subsequent comparison and alignment using lastal.</description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros_last.xml</import>
     </macros>
 
     <requirements>
-        <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">last</requirement>
     </requirements>
 
     <command detect_errors="exit_code"><![CDATA[
--- a/lastsplit.xml	Thu Mar 25 20:53:27 2021 +0000
+++ b/lastsplit.xml	Sat Nov 27 10:12:45 2021 +0000
@@ -1,13 +1,13 @@
-<tool id="last_split" name="LAST-split" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01">
+<tool id="last_split" name="LAST-split" version="@TOOL_VERSION@+galaxy0" profile="20.01">
 
     <description>finds "split alignments" (typically for DNA) or "spliced alignments" (typically for RNA).</description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros_last.xml</import>
     </macros>
 
     <requirements>
-        <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">last</requirement>
     </requirements>
 
     <command detect_errors="exit_code"><![CDATA[
--- a/lasttrain.xml	Thu Mar 25 20:53:27 2021 +0000
+++ b/lasttrain.xml	Sat Nov 27 10:12:45 2021 +0000
@@ -1,13 +1,13 @@
-<tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01">
+<tool id="last_train" name="LAST-train" version="@TOOL_VERSION@+galaxy0" profile="20.01">
 
     <description>finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences.</description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros_last.xml</import>
     </macros>
 
     <requirements>
-        <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">last</requirement>
     </requirements>
 
     <command detect_errors="exit_code"><![CDATA[
--- a/macros_last.xml	Thu Mar 25 20:53:27 2021 +0000
+++ b/macros_last.xml	Sat Nov 27 10:12:45 2021 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@LAST_CONDA_VERSION@">1205</token>
+    <token name="@TOOL_VERSION@">1205</token>
     <token name="@LAST_HELP@"><![CDATA[
         Documentation : http://last.cbrc.jp/
 
@@ -20,6 +20,11 @@
             - Train alignment parameters for unusual kinds of sequence (e.g. nanopore).
 
     ]]></token>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">last</xref>
+        </xrefs>
+    </xml>
     <xml name="citations">
         <citation type="doi">10.1101/gr.113985.110</citation>
     </xml>
--- a/maf-convert.xml	Thu Mar 25 20:53:27 2021 +0000
+++ b/maf-convert.xml	Sat Nov 27 10:12:45 2021 +0000
@@ -1,13 +1,13 @@
-<tool id="last_maf_convert" name="MAF-convert" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01">
+<tool id="last_maf_convert" name="MAF-convert" version="@TOOL_VERSION@+galaxy0" profile="20.01">
 
     <description>read MAF-format alignments and write them in another format.</description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros_last.xml</import>
     </macros>
 
     <requirements>
-        <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">last</requirement>
     </requirements>
 
     <command detect_errors="exit_code"><![CDATA[