Mercurial > repos > yating-l > jbrowsearchivecreator

diff jbrowse_hub.xml @ 4:7e471cdd9e71 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 8d93b27353190eb23490c9480e560d84cb60c973
author yating-l
date Fri, 07 Jul 2017 16:17:57 -0400
parents 25ad6770359e
children e762f4b9e4bd
line wrap: on
line diff
--- a/jbrowse_hub.xml	Wed May 31 15:45:47 2017 -0400
+++ b/jbrowse_hub.xml	Fri Jul 07 16:17:57 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="1.0">
+<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="1.0.0">
     <description>
         This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse
     </description>
@@ -80,6 +80,10 @@
                 --blastxml $f.formatChoice.BlastXML
                 #silent $prepare_json($f.formatChoice.BlastXML, extra_data_dict)
             #end if
+            #if $f.formatChoice.format_select == 'bigpsl'
+                --bigpsl $f.formatChoice.BigPsl
+                #silent $prepare_json($f.formatChoice.BigPsl, extra_data_dict)
+            #end if
             #if $f.formatChoice.format_select == 'gtf'
                 --gtf $f.formatChoice.GTF
                 #set track_color = str($f.formatChoice.track_color)
@@ -114,8 +118,9 @@
                     <param name="format_select" type="select" label="Format">
                         <option value="bam" selected="true">BAM</option>
                         <option value="bed">BED</option>
-                        <option value="blastxml">BLASTXML</option>
-                        <option value="bigwig">BIGWIG</option>
+                        <option value="blastxml">BlastXML</option>
+                        <option value="bigpsl">BigPsl</option>
+                        <option value="bigwig">BigWig</option>
                         <option value="gff3">GFF3</option>
                         <option value="gtf">GTF</option>
                     </param>
@@ -179,6 +184,15 @@
                         />
                         <param name="label" type="text" size="30" value="Blast Alignment" label="Track name" />
                     </when>
+                    <when value="bigpsl">
+                        <param
+                                format="bigpsl"
+                                name="BigPsl"
+                                type="data"
+                                label="Blat Alignments File"
+                        />
+                        <param name="label" type="text" size="30" value="Blat Alignment" label="Track name" />
+                    </when>
                     <when value="bigwig">
                         <param
                                 format="bigwig"
@@ -265,7 +279,7 @@
     </inputs>
 
     <outputs>
-        <data format="html" name="output" label="${tool.name}" />
+        <data format="jbrowsehub" name="output" label="${tool.name}" />
     </outputs>
     <tests>
         <test>