comparison piPipe.xml @ 34:02c46c8164a8 draft

Uploaded
author romaingred
date Tue, 28 Nov 2017 09:08:28 -0500
parents b9cf69322742
children
comparison
equal deleted inserted replaced
33:46d7549c1a05 34:02c46c8164a8
37 --build_miRNAs 37 --build_miRNAs
38 #else: 38 #else:
39 --miRNAs "${miRNAs.indices.fields.path}" 39 --miRNAs "${miRNAs.indices.fields.path}"
40 #end if 40 #end if
41 41
42 #if $exons.refGenomeSource == "history": 42 #if $transcripts.refGenomeSource == "history":
43 --exons "${exons.ownFile}" 43 --transcripts "${transcripts.ownFile}"
44 --build_exons 44 --build_transcripts
45 #else: 45 #else:
46 --exons "${exons.indices.fields.path}" 46 --transcripts "${transcripts.indices.fields.path}"
47 #end if 47 #end if
48 48
49 #if $TE.refGenomeSource == "history": 49 #if $TE.refGenomeSource == "history":
50 --TE "${TE.ownFile}" 50 --TE "${TE.ownFile}"
51 --build_TE 51 --build_TE
185 </when> 185 </when>
186 <when value="history"> 186 <when value="history">
187 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> 187 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
188 </when> 188 </when>
189 </conditional> 189 </conditional>
190 <conditional name="exons"> 190 <conditional name="transcripts">
191 <param name="refGenomeSource" type="select" label="Will you select exons database from your history or use a built-in index?"> 191 <param name="refGenomeSource" type="select" label="Will you select transcripts database from your history or use a built-in index?">
192 <option value="indexed">Use a built-in index</option> 192 <option value="indexed">Use a built-in index</option>
193 <option value="history">Use one from the history</option> 193 <option value="history">Use one from the history</option>
194 </param> 194 </param>
195 <when value="indexed"> 195 <when value="indexed">
196 <param name="indices" type="select" label="Select a exons reference"> 196 <param name="indices" type="select" label="Select a transcripts reference">
197 <options from_data_table="bwa_indexes"> 197 <options from_data_table="bwa_indexes">
198 <filter type="sort_by" column="2" /> 198 <filter type="sort_by" column="2" />
199 <validator type="no_options" message="No indexes are available" /> 199 <validator type="no_options" message="No indexes are available" />
200 </options> 200 </options>
201 </param> 201 </param>