diff lastz.xml @ 3:c3767eaae954 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413

--- a/lastz.xml	Fri Mar 02 12:06:35 2018 -0500
+++ b/lastz.xml	Thu May 17 04:28:59 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="lastz_wrapper_2" name="LASTZ" version="1.3">
+<tool id="lastz_wrapper_2" name="LASTZ" version="1.3.1">
     <description>: align long sequences</description>
     <macros>
         <import>lastz_macros.xml</import>
@@ -7,6 +7,7 @@
         <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>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         lastz
@@ -18,7 +19,7 @@
                 '${where_to_look.nomirror}'
             #end if
         #else:
-            '${query}'
+            @query_input@
         #end if
 
 ## WHERE TO LOOK --------------------------------
@@ -279,7 +280,7 @@
     </configfiles>
     <inputs>
         <expand macro="target_input"/>
-        <param name="query" format="fasta,fastq" type="data" label="Select QUERY sequence(s)" help="These are the sequences that you are aligning against TARGET"/>
+        <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"/>
 
         <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">
@@ -596,6 +597,38 @@
             <param name="format" value="general_def" />
             <output name="output" value="test3.out" />
         </test>
+        <test>
+            <param name="ref_source" value="history" />
+            <param name="target" value="chrM_mouse.fa.gz" />
+            <param name="query" value="chrM_human.fa.gz" />
+            <param name="strand" value="--strand=both" />
+            <param name="format" value="blastn" />
+            <output name="output" value="test4.out" />
+        </test>
+        <test>
+            <param name="ref_source" value="history" />
+            <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
+            <param name="query" ftype="fastq.bz2" value="chrM_mouse.fq.bz2" />
+            <param name="strand" value="--strand=both" />
+            <param name="format" value="blastn" />
+            <output name="output" value="test5.out" />
+        </test>
+        <test>
+            <param name="ref_source" value="history" />
+            <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
+            <param name="query" ftype="fastq.gz" value="chrM_mouse.fq.gz" />
+            <param name="strand" value="--strand=both" />
+            <param name="format" value="blastn" />
+            <output name="output" value="test5.out" />
+        </test>
+        <test>
+            <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="strand" value="--strand=both" />
+            <param name="format" value="blastn" />
+            <output name="output" value="test5.out" />
+        </test>
     </tests>
 
     <help><![CDATA[