# HG changeset patch
# User bgruening
# Date 1499882710 14400
# Node ID 53e9709776a0da7c37013bf34a98b069095f4a71
# Parent  570e7e9c19a560190a6d127d7121eb0f322788e9
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3103ebed1a420c7d3415b67ef532ea579edf9faa

diff -r 570e7e9c19a5 -r 53e9709776a0 salmon.xml
--- a/salmon.xml	Fri Jun 30 05:45:09 2017 -0400
+++ b/salmon.xml	Wed Jul 12 14:05:10 2017 -0400
@@ -132,7 +132,6 @@
             #if $adv.forgettingFactor:
                 --forgettingFactor $adv.forgettingFactor
             #end if
-            $adv.writeMappings
             #if str($adv.maxOcc):
                 --maxOcc $adv.maxOcc
             #end if
@@ -167,6 +166,9 @@
                 --vbPrior $adv.vbPrior
             #end if
             $adv.writeUnmappedNames
+            #if str($adv.writeMappings):
+                $adv.writeMappings > ${output_sam}
+            #end if
 ]]>
     </command>
 
@@ -239,7 +241,7 @@
         <section name="adv" title="Additional Options">
             <param argument="--writeMappings" type="boolean" truevalue="--writeMappings" falsevalue="" checked="False"
                 label="Write Mappings"
-                help=" Setting this option then the quasi-mapping results will be written out in SAM-cpmpatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead." />
+                help="If this option is set to 'Yes', then the quasi-mapping results will be written out in SAM-compatible format. By default, output is directed to stdout." />
             <param argument="--incompatPrior" type="float" optional="True" value="9.9999999999999995e-21"
                 label="Incompatible Prior"
                 help="This option sets the prior probability that an alignment that disagrees with the specified library type (--libType) results from the true fragment origin. Setting this to 0 specifies that alignments that disagree with the library type should be 'impossible', while setting it to 1 says that alignments that disagree with the library type are no less likely than those that do" />
@@ -336,6 +338,9 @@
         <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">
             <filter>geneMap</filter>
         </data>
+        <data name="output_sam" format="sam" label="${tool.name} on ${on_string} (SAM format)">
+            <filter>adv['writeMappings']</filter>
+        </data>
     </outputs>
 
     <tests>