changeset 10:3e1ea2facca6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2"

--- a/lastz.xml	Fri Apr 02 17:18:40 2021 +0000
+++ b/lastz.xml	Sat Nov 27 10:41:24 2021 +0000
@@ -1,16 +1,22 @@
-<tool id="lastz_wrapper_2" name="LASTZ" version="1.3.3">
+<tool id="lastz_wrapper_2" name="LASTZ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>: align long sequences</description>
     <macros>
         <import>lastz_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <requirements>
-        <requirement type="package" version="@LASTZ_CONDA_VERSION@">lastz</requirement>
-        <requirement type="package" version="1.7">samtools</requirement>
-        <requirement type="package" version="3.4.2">r-base</requirement>
-        <requirement type="package" version="1.0.6">bzip2</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">lastz</requirement>
+        <requirement type="package" version="1.14">samtools</requirement>
+        <requirement type="package" version="3.6.3">r-base</requirement>
+        <requirement type="package" version="1.0.8">bzip2</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        lastz
+        #if $lastz_32:
+            lastz_32
+        #else:
+            lastz
+        #end if
+
         @TARGET_INPUT_COMMAND_LINE@
         ## If --self is set: perform self alignment and ignore the query
         #if $where_to_look.self:
@@ -291,7 +297,7 @@
     <inputs>
         <expand macro="target_input"/>
         <param name="query" format="fasta,fastq,fasta.gz,fastq.gz,fastq.bz2" type="data" label="Select QUERY sequence(s)" help="These are the sequences that you are aligning against TARGET"/>
-
+        <param name="lastz_32" type="boolean" checked="false" label="Use lastz_32" help="It is highly recommended to use lastz_32 instead of lastz if the refernece genome size is greater than 2G"/>
         <section name="where_to_look" expanded="False" title="Where to look">
             <param name="strand" type="select" display="radio" label="which strand to search" argument="--strand" help="Search both strands or choose plus or minus">
                 <option value="--strand=both" selected="True">Both</option>
@@ -645,6 +651,7 @@
             <param name="ref_source" value="history" />
             <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
             <param name="query" ftype="fastq" value="chrM_mouse.fq" />
+            <param name="lastz_32" value="true" />
             <param name="strand" value="--strand=both" />
             <param name="format" value="blastn" />
             <output name="output" value="test5.out" />

--- a/lastz_d.xml	Fri Apr 02 17:18:40 2021 +0000
+++ b/lastz_d.xml	Sat Nov 27 10:41:24 2021 +0000
@@ -1,11 +1,12 @@
-<tool id="lastz_d_wrapper" name="LASTZ_D" version="1.3.2">
+<tool id="lastz_d_wrapper" name="LASTZ_D" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>: estimate substitution scores matrix</description>
     <macros>
     	<import>lastz_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <requirements>
-        <requirement type="package" version="@LASTZ_CONDA_VERSION@">lastz</requirement>
-        <requirement type="package" version="1.0.6">bzip2</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">lastz</requirement>
+        <requirement type="package" version="1.0.8">bzip2</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         lastz_D

--- a/lastz_macros.xml	Fri Apr 02 17:18:40 2021 +0000
+++ b/lastz_macros.xml	Sat Nov 27 10:41:24 2021 +0000
@@ -1,5 +1,6 @@
 <macros>
-    <token name="@LASTZ_CONDA_VERSION@">1.0.4</token>
+    <token name="@TOOL_VERSION@">1.04.15</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@TARGET_INPUT_COMMAND_LINE@"><![CDATA[
         #if $source.ref_source=="history":
             #if $source.target.is_of_type('fasta.gz'):
@@ -22,6 +23,11 @@
         #end if
         ]]>
     </token>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">lastz</xref>
+        </xrefs>
+    </xml>
     <xml name="target_input">
         <conditional name="source">
             <param name="ref_source" type="select" label="Select TARGET sequnce(s) to align against" help="If your TARGET is in history, choose 'from your history' option">