Mercurial > repos > rmarenco > hubarchivecreator

diff hubArchiveCreator.xml @ 21:884ee2a71680 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
author yating-l
date Wed, 12 Apr 2017 15:05:33 -0400
parents 40469b265ddb
children 7ddf651457df
line wrap: on
line diff
--- a/hubArchiveCreator.xml	Fri Jan 20 17:12:03 2017 -0500
+++ b/hubArchiveCreator.xml	Wed Apr 12 15:05:33 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.0">
+<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.1">
     <description>
         This Galaxy tool permits to prepare your files to be ready for
         Assembly Hub visualization.
@@ -99,10 +99,10 @@
                         #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
                                                 extra_data_dict)
                     #end if
-                    #if $f.formatChoice.bedChoice.bed_select == "bigpsl_option"
-                        --bigpsl $f.formatChoice.bedChoice.bigPsl
-                        #silent $prepare_json($f.formatChoice.bedChoice.bigPsl, $index_track_final,
-                                                extra_data_dict)
+                    #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
+                        --bedBlastAlignments $f.formatChoice.bedChoice.BED_blast_alignment
+                        #silent $prepare_json($f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,                              
+                                             extra_data_dict)
                     #end if
                 #end if
                 #if $f.formatChoice.format_select == "psl"
@@ -126,6 +126,11 @@
                     #silent $prepare_json($f.formatChoice.GTF, $index_track_final,
                                              extra_data_dict)
                 #end if
+                #if $f.formatChoice.format_select == "bigpsl"
+                    --bigpsl $f.formatChoice.BIGPSL
+                    #silent $prepare_json($f.formatChoice.BIGPSL, $index_track_final,                       
+                                            extra_data_dict)
+                #end if
             #end for
         #end for
 
@@ -176,6 +181,7 @@
                         <option value="bigwig">BIGWIG</option>
                         <option value="gff3">GFF3</option>
                         <option value="gtf">GTF</option>
+                        <option value="bigpsl">BigPsl</option>
                     </param>
 
                     <when value="bam">
@@ -193,14 +199,14 @@
                                 </valid>
                             </sanitizer>
                         </param>
-                    </when>
+                    </when>     
                     <when value="bed">
                         <conditional name="bedChoice">
                             <param name="bed_select" type="select" label="Bed Choice">
                                 <option value="bed_generic" selected="true">BED Generic (bed3+)</option>
                                 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
                                 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
-                                <option value="bigpsl_option">bigPsl (bed12+12 / bigPsl.as)</option>
+                                <option value="bed_blast_alignment_option">BED Blast alignments (bed12+12 / bigPsl.as)</option>
                             </param>
                             <when value="bed_generic">
                                 <param
@@ -227,12 +233,12 @@
                                         label="Bed Splice Junctions (Bed12+1) File"
                                 />
                             </when>
-                            <when value="bigpsl_option">
+                            <when value="bed_blast_alignment_option">
                                 <param
                                         format="bed"
-                                        name="bigPsl"
+                                        name="BED_blast_alignment"
                                         type="data"
-                                        label="bigPsl (Bed12+12) File"
+                                        label="Bed Blast Alignments (Bed12+12) File"
                                 />
                             </when>
                         </conditional>
@@ -304,6 +310,21 @@
                             </sanitizer>
                         </param>
                     </when>
+                    <when value="bigpsl">
+                        <param 
+                                format="bigpsl"
+                                name="BIGPSL"
+                                type="data"
+                                label="bigPsl File"
+                        />
+                        <param name="track_color" type="color" label="Track color" value="#000000">
+                            <sanitizer>
+                                <valid initial="string.letters,string.digits">
+                                    <add value="#"/>
+                                </valid>
+                            </sanitizer>
+                        </param>
+                    </when>   
                 </conditional>
             </repeat>
         </repeat>