diff metaphlan2.xml @ 9:31dd7ace2be4 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 90c51a29d5aaab3f8dea67ac12098dc386e23b4e-dirty

--- a/metaphlan2.xml	Wed Oct 28 12:41:43 2015 -0400
+++ b/metaphlan2.xml	Thu Nov 05 08:44:11 2015 -0500
@@ -105,28 +105,28 @@
 
         <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/>
 
-        <param name="bowtie2_output" type='boolean' checked="true" truevalue='' falsevalue='--no_map' label="Store the output of BowTie2?" help="" />
-        <param name="sam_output" type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Output a sam file?" help="" />
-        <param name="biom_output" type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Output a biom file?" help="" />
+        <param name="bowtie2_output" type='boolean' checked="true" truevalue="" falsevalue='--no_map' label="Store the output of BowTie2?" help="" />
+        <param name="sam_output" type='boolean' label="Output a sam file?" help="" />
+        <param name="biom_output" type='boolean' label="Output a biom file?" help="" />
     </inputs>
 
     <outputs>
-        <data format_source="txt" name="output_file" 
+        <data format="txt" name="output_file" 
             metadata="input_sequence_file" 
             label="Profile of communities on ${on_string} (MetaPhlAn)" />
 
-        <data format_source="bowtie2" name="bowtie2_output_file" 
+        <data format="bowtie2" name="bowtie2_output_file" 
             metadata="input_sequence_file" 
             label="Bowtie2 output on ${on_string} (MetaPhlAn)">
-            <filter>!bowtie2_output</filter>
+            <filter>bowtie2_output != '--no_map' </filter>
         </data>
 
-        <data format_source="sam" name="sam_output_file" 
+        <data format="sam" name="sam_output_file" 
             metadata="input_sequence_file" 
             label="Sam output on ${on_string} (MetaPhlAn)">
             <filter>sam_output</filter>
         </data>
-        <data format_source="biom" name="biom_output_file" 
+        <data format="biom" name="biom_output_file" 
             metadata="input_sequence_file" 
             label="Biom output on ${on_string} (MetaPhlAn)">
             <filter>biom_output</filter>
@@ -136,6 +136,18 @@
     <tests>
         <test>
             <param name="input_file" value="input_sequences.fastq"/>
+            <param name="analysis_type_select" value="rel_ab" />
+            <param name="taxonomic_level" value="a" />
+            <param name="min_cu_len" value="2000" />
+            <param name="min_alignment_len" value="0" />
+            <param name="ignore_viruses" value="" />
+            <param name="ignore_eukaryotes" value="" />
+            <param name="ignore_bacteria" value="" />
+            <param name="ignore_archaea" value="" />
+            <param name="stat_q" value="0.1" />
+            <param name="bowtie2_output" value='--no_map' />
+            <param name="sam_output" value='False' />
+            <param name="biom_output" value='False' />
             <output name="output_file" file="profiled_metagenome.txt"/>
         </test>
     </tests>