Mercurial > repos > iuc > qiime_split_libraries

diff split_libraries.xml @ 7:481efc8a2fe2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 358f82bc5a70186b8fc917fe0f5323a330051b8e
author iuc
date Tue, 30 Apr 2019 09:31:55 -0400
parents 6f2a0b6a8da2
children 2aca5aae5d10
line wrap: on
line diff
--- a/split_libraries.xml	Tue Oct 30 20:03:59 2018 -0400
+++ b/split_libraries.xml	Tue Apr 30 09:31:55 2019 -0400
@@ -110,8 +110,8 @@
         <data name="sequences" format="fasta" from_work_dir="split_libraries/*.fna" label="${tool.name} on ${on_string}: sequences"/>
         <data name="log" format="txt" from_work_dir="split_libraries/split_library_log.txt" label="${tool.name} on ${on_string}: log"/>
         <data name="histograms" format="txt" from_work_dir="split_libraries/histograms.txt" label="${tool.name} on ${on_string}: histograms"/>
-        <data name="quality" format="qual,qual454,qualillumina,qualsolexa,qualsolid" from_work_dir="split_libraries/*.qual" label="${tool.name} on ${on_string}: quality">
-            <filter>add_qual['record_qual_scores']!=""</filter>
+        <data name="quality" format_source="qual" from_work_dir="split_libraries/*.qual" label="${tool.name} on ${on_string}: quality">
+            <filter>'record_qual_scores' in add_qual and add_qual['record_qual_scores']</filter>
         </data>
     </outputs>
     <tests>
@@ -119,7 +119,7 @@
             <param name="map" value="split_libraries/mapping_file.txt"/>
             <param name="fasta" value="split_libraries/reads_1.fna,split_libraries/reads_2.fna"/>
             <param name="add_qual_test" value="true"/>
-            <param name="qual" value="split_libraries/reads_1.qual,split_libraries/reads_2.qual"/>
+            <param name="qual" ftype="qualillumina" value="split_libraries/reads_1.qual,split_libraries/reads_2.qual"/>
             <param name="min_qual_score" value="25"/>
             <param name="qual_score_window" value="0"/>
             <param name="discard_bad_windows" value=""/>
@@ -150,7 +150,7 @@
             </output>
             <output name="log" file="split_libraries/split_library_log"/>
             <output name="histograms" file="split_libraries/histograms.txt"/>
-            <output name="quality">
+            <output name="quality" ftype="qualillumina">
                 <assert_contents>
                     <has_text text="PC.634_1" />
                     <has_text text="bc_diffs" />