Mercurial > repos > yating-l > hubarchivecreator

diff hubArchiveCreator.xml @ 55:ba9997c847dc draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
author yating-l
date Wed, 17 May 2017 13:16:57 -0400
parents 4a58094b051e
children b39dd0b5a166
line wrap: on
line diff
--- a/hubArchiveCreator.xml	Tue May 16 18:09:00 2017 -0400
+++ b/hubArchiveCreator.xml	Wed May 17 13:16:57 2017 -0400
@@ -5,9 +5,10 @@
     </description>
 
     <requirements>
-        <requirement type="package" version="1.0">ucsc_tools_340</requirement>
+        <requirement type="package" version="340">ucsc_hac</requirement>
         <requirement type="package" version="1.2">samtools</requirement>
         <requirement type="package" version="340">ucsc_bigwig</requirement>
+        <requirement type="package" version="340">ucsc_bigbed</requirement>
     </requirements>
 
     <stdio>
@@ -127,6 +128,11 @@
                     #silent $prepare_json($f.formatChoice.BIGWIG, $index_track_final,
                                             extra_data_dict)
                 #end if
+                #if $f.formatChoice.format_select == "bigbed"
+                    --bigbed $f.formatChoice.BIGBED
+                    #silent $prepare_json($f.formatChoice.BIGBED, $index_track_final,
+                                            extra_data_dict)
+                #end if
                 #if $f.formatChoice.format_select == "gff3"
                     --gff3 $f.formatChoice.GFF3
                     #silent $prepare_json($f.formatChoice.GFF3, $index_track_final,
@@ -186,6 +192,7 @@
                         <option value="bed">BED</option>
                         <option value="psl">PSL</option>
                         <option value="bigwig">BIGWIG</option>
+                        <option value="bigbed">BIGBED</option>
                         <option value="gff3">GFF3</option>
                         <option value="gtf">GTF</option>
                     </param>
@@ -308,6 +315,22 @@
                             </sanitizer>
                         </param>
                     </when>
+                    <when value="bigbed">
+                        <param
+                                format="bigbed"
+                                name="BIGBED"
+                                type="data"
+                                label="BIGBED File"
+                        />
+                        <param name="longLabel" type="text" size="30" label="Track name" />
+                        <param name="track_color" type="color" label="Track color" value="#000000">
+                            <sanitizer>
+                                <valid initial="string.letters,string.digits">
+                                    <add value="#"/>
+                                </valid>
+                            </sanitizer>
+                        </param>
+                    </when>
                     <when value="gff3">
                         <param
                                 format="gff3"