diff salmon.xml @ 9:2c0ca397d302 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72-dirty

--- a/salmon.xml	Thu Aug 23 15:58:26 2018 -0400
+++ b/salmon.xml	Sat Jul 27 12:37:47 2019 -0400
@@ -18,6 +18,7 @@
             </param>
         </xml>
         <token name="@VERSION@">0.11.2</token>
+        <token name="@IDX_VERSION@">q5</token>
     </macros>
 
     <requirements>
@@ -230,8 +231,9 @@
             </param>
             <when value="indexed">
                 <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy admin">
-                    <options from_data_table="salmon_indexes">
+                    <options from_data_table="salmon_indexes_versioned">
                         <filter type="sort_by" column="2"/>
+                        <filter type="static_value" column="4" value="@IDX_VERSION@" />
                         <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                     </options>
                 </param>
@@ -441,6 +443,28 @@
                 </assert_contents>
             </output>
         </test>
+        <test> <!--test use of built-in index-->
+            <param name="single_or_paired_opts" value="paired" />
+            <param name="input_mate1" value="reads_1.fastq" />
+            <param name="input_mate2" value="reads_2.fastq" />
+            <param name="biasCorrect" value="False" />
+            <param name="TranscriptSource" value="indexed" />
+            <param name="index" value="hg19_transcript_subset" />
+            <output name="output_quant">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="NM_001168316" />
+                    <has_text text="NM_174914" />
+                    <has_text text="NM_018953" />
+                    <has_text text="NR_003084" />
+                    <has_text text="NM_017410" />
+                    <has_text text="NM_153693" />
+                    <has_text text="NR_031764" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+        </test>
         <test> <!-- gzipped input -->
             <param name="single_or_paired_opts" value="paired" />
             <param name="input_mate1" value="reads_1.fastq.gz" ftype="fastqsanger.gz" />