Mercurial > repos > iuc > last

changeset 7:eca7ac1eb423 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit ddb5e058a7877e627ed24ef8cb9a046ccb450cb4
author iuc
date Mon, 23 Oct 2023 20:45:02 +0000
parents 19c265784f35
children
files lastal.xml lastdb.xml lastsplit.xml lasttrain.xml macros_last.xml maf-convert.xml
diffstat 6 files changed, 23 insertions(+), 45 deletions(-) [+]
line wrap: on
line diff
--- a/lastal.xml	Sat Nov 27 10:12:45 2021 +0000
+++ b/lastal.xml	Mon Oct 23 20:45:02 2023 +0000
@@ -1,15 +1,10 @@
-<tool id="last_al" name="LASTal" version="@TOOL_VERSION@+galaxy1" profile="20.01">
-
+<tool id="last_al" name="LASTal" version="@TOOL_VERSION@+galaxy2" 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="@TOOL_VERSION@">last</requirement>
-    </requirements>
-
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         set -e -o pipefail; 
 
--- a/lastdb.xml	Sat Nov 27 10:12:45 2021 +0000
+++ b/lastdb.xml	Mon Oct 23 20:45:02 2023 +0000
@@ -1,15 +1,10 @@
-<tool id="last_db" name="LASTdb" version="@TOOL_VERSION@+galaxy0" profile="20.01">
-
+<tool id="last_db" name="LASTdb" version="@TOOL_VERSION@+galaxy1" 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="@TOOL_VERSION@">last</requirement>
-    </requirements>
-
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         set -e -o pipefail; 
 
@@ -140,9 +135,7 @@
     </inputs>
 
     <outputs>
-        <data name="outfile" format="lastdb">
-            <discover_datasets pattern="__designation__" directory="ref_genome"/>
-        </data>
+        <data name="outfile" format="lastdb"/>
     </outputs>
 
     <tests>
--- a/lastsplit.xml	Sat Nov 27 10:12:45 2021 +0000
+++ b/lastsplit.xml	Mon Oct 23 20:45:02 2023 +0000
@@ -1,15 +1,10 @@
-<tool id="last_split" name="LAST-split" version="@TOOL_VERSION@+galaxy0" profile="20.01">
-
+<tool id="last_split" name="LAST-split" version="@TOOL_VERSION@+galaxy1" 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="@TOOL_VERSION@">last</requirement>
-    </requirements>
-
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         #if $db_opts.db_opts_input == 'lastdb'
             ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' &&
--- a/lasttrain.xml	Sat Nov 27 10:12:45 2021 +0000
+++ b/lasttrain.xml	Mon Oct 23 20:45:02 2023 +0000
@@ -1,15 +1,10 @@
-<tool id="last_train" name="LAST-train" version="@TOOL_VERSION@+galaxy0" profile="20.01">
-
+<tool id="last_train" name="LAST-train" version="@TOOL_VERSION@+galaxy1" 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="@TOOL_VERSION@">last</requirement>
-    </requirements>
-
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         set -e -o pipefail; 
         #if $db_opts.db_opts_input == 'lastdb'
--- a/macros_last.xml	Sat Nov 27 10:12:45 2021 +0000
+++ b/macros_last.xml	Mon Oct 23 20:45:02 2023 +0000
@@ -1,7 +1,7 @@
 <macros>
     <token name="@TOOL_VERSION@">1205</token>
     <token name="@LAST_HELP@"><![CDATA[
-        Documentation : http://last.cbrc.jp/
+        Documentation : https://gitlab.com/mcfrith/last
 
         LAST finds similar regions between sequences.
 
@@ -20,6 +20,11 @@
             - Train alignment parameters for unusual kinds of sequence (e.g. nanopore).
 
     ]]></token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">last</requirement>
+        </requirements>
+    </xml>
     <xml name="bio_tools">
         <xrefs>
             <xref type="bio.tools">last</xref>
@@ -36,7 +41,7 @@
               <option value="lastdb" selected="true">LAST database from history</option>
             </param>
             <when value="db">
-                <param name="database" type="select" multiple="true" label="LAST database">
+                <param name="database" type="select" label="LAST database">
                     <options from_data_table="lastdb" />
                 </param>
             </when>
--- a/maf-convert.xml	Sat Nov 27 10:12:45 2021 +0000
+++ b/maf-convert.xml	Mon Oct 23 20:45:02 2023 +0000
@@ -1,15 +1,10 @@
-<tool id="last_maf_convert" name="MAF-convert" version="@TOOL_VERSION@+galaxy0" profile="20.01">
-
+<tool id="last_maf_convert" name="MAF-convert" version="@TOOL_VERSION@+galaxy1" 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="@TOOL_VERSION@">last</requirement>
-    </requirements>
-
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         maf-convert