Mercurial > repos > romaingred > pirna_pipeline
comparison piPipe.xml @ 34:02c46c8164a8 draft
Uploaded
author | romaingred |
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date | Tue, 28 Nov 2017 09:08:28 -0500 |
parents | b9cf69322742 |
children |
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33:46d7549c1a05 | 34:02c46c8164a8 |
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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> |