Changed the TBprofiler wrapper target version 2.1.0 to version… (#2463)

Changed the TBprofiler wrapper target version 2.1.0 to version 2.4
galaxyproject · Jul 16, 2019 · da74c7f · da74c7f
2 parents df0ef2f + f31eeee
commit da74c7f
Showing 1 changed file with 13 additions and 15 deletions.
diff --git a/tools/tb-profiler/tb_profiler_profile.xml b/tools/tb-profiler/tb_profiler_profile.xml
@@ -1,7 +1,7 @@
-<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="2.1.0">
-    <description>Infer strain types and drug resistance markers from sequences</description>	
+<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="2.4">
+    <description>Infer strain types and drug resistance markers from sequences</description>
     <requirements>
-        <requirement type="package" version="2.1.0">tb-profiler</requirement>
+        <requirement type="package" version="2.4">tb-profiler</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
@@ -60,7 +60,7 @@
             && mv results/tbprofiler.results.txt '${output_txt}'
         #end if 
 
-    ]]></command>
+    ]]>    </command>
     <inputs>
         <param name="platform" type="select" label="Platform">
             <option value="Illumina" selected="true">Illumina</option>
@@ -82,7 +82,7 @@
             </when>
             <when value="single_fastq">
                 <param label="Reads" name="fastq" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
-            </when>            
+            </when>
             <when value="bam">
                 <param name="bam_input" type="data" format="bam" label="Bam" help="Warning!!!: The BAM files must have been created using the ensembl version of the genome."/>
             </when>
@@ -104,9 +104,7 @@
                     <option value="high">High</option>
                     <option value="optimise">Optimise</option>
                 </param>
-                <param label="Minimum coverage fraction to infer deletion" type="float"
-                        help="Used to infer a deletion if the fraction of a gene covered falls below this value."
-                        argument="--min_gene_frac" value="0.9" />
+                <param label="Minimum coverage fraction to infer deletion" type="float" help="Used to infer a deletion if the fraction of a gene covered falls below this value." argument="--min_gene_frac" value="0.9" />
 
                 <param name="min_depth" label="Min Depth" type="integer" value="10" help="Minimum depth required to call variant. Bases with depth below this cutoff will be marked as missing (default: 10)"/>
                 <param name="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)">
@@ -142,9 +140,9 @@
             <output name="output_txt">
                 <assert_contents>
                     <has_line line="Drug-resistance: Drug-resistant" />
-		    <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
-                    <has_line line="rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
-                    <has_line line="763031&#009;Rv0667&#009;c.3225T>C&#009;1.000" />
+                    <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
+                    <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
+                    <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;1.000" />
                 </assert_contents>
             </output>
         </test>
@@ -157,9 +155,9 @@
             <output name="output_txt">
                 <assert_contents>
                     <has_line line="Drug-resistance: Drug-resistant" />
-		    <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
-                    <has_line line="rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
-                    <has_line line="763031&#009;Rv0667&#009;c.3225T>C&#009;1.000" />
+                    <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
+                    <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
+                    <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;1.000" />
                 </assert_contents>
             </output>
         </test>
@@ -172,7 +170,7 @@ The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2
 
 Produces a JSON output file by default.
 
-    ]]></help>
+    ]]>    </help>
     <citations>
         <citation type="bibtex">
 @UNPUBLISHED{Phelan2016,