diff lastz.xml @ 5:ec4affe27298 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c"

--- a/lastz.xml	Fri May 18 16:58:24 2018 -0400
+++ b/lastz.xml	Fri Apr 02 17:18:09 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="lastz_wrapper_2" name="LASTZ" version="1.3.2">
+<tool id="lastz_wrapper_2" name="LASTZ" version="1.3.3">
     <description>: align long sequences</description>
     <macros>
         <import>lastz_macros.xml</import>
@@ -255,11 +255,13 @@
             --format=BLASTN-
         #elif str( $output_format.out.format ) == "general_full":
             '--format=general-:${output_format.out.fields}'
+        #elif str( $output_format.out.format ) == "differences":
+            '--format=differences'
         #end if
         --action:target=multiple
         $output_format.rplot
         #if str( $output_format.out.format ) == "bam":
-            | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '${output}'
+            | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '${output}'
         #else:
             > '${output}'
         #end if
@@ -492,6 +494,7 @@
                     <option value="general_full">Customized general (‑‑format=general[:fields])</option>
                     <option value="maf">MAF (--format=maf)</option>
                     <option value="blastn">blastn (--format=BLASTN)</option>
+                    <option value="differences">Differences (--format=differences)</option>
                 </param>
                 <when value="bam">
                     <param name="bam_options" type="select" display="radio" argument="--format=sam, --format=softsam" label="Select a BAM flavor to output" help="Lastz actually outputs SAM data but Galaxy converts it into BAM to save space. For alignments that don't reach the end of a query, ‑‑format=sam uses 'hard clipping', while ‑‑format=softsam uses 'soft clipping'. See the section on 'clipped alignment' in the SAM specification for an explanation of what this means. The options ‑‑format=sam- and ‑‑format=softsam- suppress the SAM header lines. This makes them suitable for concatenating output from multiple runs. If you need to specify readgroup information: use AddOrEplaceReadGroups from Picard package">
@@ -567,6 +570,9 @@
                 <when value="blastn">
                     <!-- Do nothing -->
                 </when>
+                <when value="differences">
+                    <!-- Do nothing -->
+                </when>
             </conditional>
             <param name="rplot" type="boolean" truevalue="--rdotplot=plot.r" falsevalue="" checked="false" argument="--rdotplot" label="Create a dotplot representation of alignments?" help="The dotplot is only useful if query and target contain exactly one sequence each"/>
         </section>
@@ -574,8 +580,9 @@
     <outputs>
         <data format="tabular" name="output" label="${tool.name} on ${on_string}: mapped reads">
             <change_format>
-                 <when input="output_format.out.format" value="bam" format="bam" />
-                  <when input="output_format.out.format" value="maf" format="maf" />
+                <when input="output_format.out.format" value="bam" format="bam" />
+                <when input="output_format.out.format" value="maf" format="maf" />
+                <when input="output_format.out.format" value="differences" format="interval" />
             </change_format>
         </data>
         <data format="png" name="out_plot" label="${tool.name} on ${on_string}: dot plot">
@@ -642,6 +649,14 @@
             <param name="format" value="blastn" />
             <output name="output" value="test5.out" />
         </test>
+        <test>
+            <param name="ref_source" value="cached" />
+            <param name="target_2bit" value="phiX174" />
+            <param name="query" value="phiX_split.fasta" />
+            <param name="strand" value="--strand=both" />
+            <param name="format" value="differences" />
+            <output name="output" value="test6.out" />
+        </test>
     </tests>
 
     <help><![CDATA[