Mercurial > repos > bebatut > sortmerna

diff sortmerna.xml @ 7:152bd01a4e76 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit ac257f4227abec655c923fe377af182588b6d7bf-dirty
author bebatut
date Thu, 05 Nov 2015 09:09:06 -0500
parents 817fb14fc739
children 941ebfa59d1a
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--- a/sortmerna.xml	Thu Nov 05 08:31:34 2015 -0500
+++ b/sortmerna.xml	Thu Nov 05 09:09:06 2015 -0500
@@ -121,7 +121,7 @@
                 <option value="">No</option>
             </param>
             <when value="--fastx">
-                <param name='fastx_rejected' type='boolean' label="Conserve rejected reads?" help=""/>
+                <param name='fastx_rejected' type='boolean' checked="true" label="Conserve rejected reads?" help=""/>
             </when>
         </conditional>
 
@@ -236,11 +236,27 @@
             <param name="input_sequence_file" value="input_sequences.fastq" ftype="fastq"/>
             <param name="databases_selector" value="history" />
             <param name="databases_name" value="db.fasta" ftype="fasta"/>
+            <param name="fastx_test" value="--fastx" />
+            <param name='fastx_rejected' value="True"/>
+            <param name="sam_test" value="" />
+            <param name="blast_format" value="--blast 3" />
+            <param name='log' value="" />
+            <param name="report_type" value="best" />
+            <param name="report_best_type" value="1" /> 
+            <param name="report_best_min_lis" value="2" />
+            <param name="e_value" value="1" />
+            <param name="match" value="2" />
+            <param name="mismatch" value="-3" />
+            <param name="gap_open" value="5" />
+            <param name="gap_ext" value="2" />
+            <param name="ambiguous_letter" value="-3" />
+            <param name="strand" value="both" />
+            <param name="seed_length" value="18" />
+            <param name="max_pos" value="10000" />
             
             <output name="aligned_sequence_file" file="aligned_sequences.fastq" ftype="fastq"/>
             <output name="rejected_sequence_file" file="rejected_sequences.fastq" ftype="fastq"/>
             <output name="blast_output_file" file="blast_output.tabular" ftype="tabular"/>
-            <output name="sam_alignment_file" file="sam_alignments.sam" ftype="sam"/>
         </test>
     </tests>