Mercurial > repos > devteam > cuffquant
comparison cuffquant_wrapper.xml @ 2:b2ee2bef1926 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
| author | devteam |
|---|---|
| date | Tue, 07 Feb 2017 18:40:42 -0500 |
| parents | 986b63735a5e |
| children | 6dc45faebc1d |
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| 1:986b63735a5e | 2:b2ee2bef1926 |
|---|---|
| 1 <tool id="cuffquant" name="Cuffquant" version="@VERSION@.0"> | 1 <tool id="cuffquant" name="Cuffquant" version="@VERSION@.0"> |
| 2 <!-- Wrapper supports Cuffdiff versions 2.2.1 --> | 2 <!-- Wrapper supports Cuffdiff versions 2.2.1 --> |
| 3 <description>Precompute gene expression levels</description> | 3 <description>Precompute gene expression levels</description> |
| 4 <expand macro="requirements" /> | |
| 5 <expand macro="stdio" /> | |
| 6 <macros> | 4 <macros> |
| 7 <import>cuff_macros.xml</import> | 5 <import>cuff_macros.xml</import> |
| 8 </macros> | 6 </macros> |
| 7 <expand macro="requirements" /> | |
| 8 <expand macro="stdio" /> | |
| 9 <version_command>cuffquant 2>&1 | head -n 1</version_command> | 9 <version_command>cuffquant 2>&1 | head -n 1</version_command> |
| 10 <command> | 10 <command> |
| 11 cuffquant | 11 cuffquant |
| 12 --no-update-check | 12 --no-update-check |
| 13 --num-threads=\${GALAXY_SLOTS:-4} | 13 --num-threads=\${GALAXY_SLOTS:-4} |
| 25 ## Bias correction? | 25 ## Bias correction? |
| 26 #if $bias_correction.do_bias_correction == "Yes": | 26 #if $bias_correction.do_bias_correction == "Yes": |
| 27 -b | 27 -b |
| 28 #if $bias_correction.seq_source.index_source == "history": | 28 #if $bias_correction.seq_source.index_source == "history": |
| 29 ## Custom genome from history. | 29 ## Custom genome from history. |
| 30 $bias_correction.seq_source.ref_file | 30 '$bias_correction.seq_source.ref_file' |
| 31 #else: | 31 #else: |
| 32 ## Built-in genome. | 32 ## Built-in genome. |
| 33 "${ bias_correction.seq_source.index.fields.path }" | 33 '${bias_correction.seq_source.index.fields.path}' |
| 34 #end if | 34 #end if |
| 35 #end if | 35 #end if |
| 36 | 36 |
| 37 $length_correction | 37 $length_correction |
| 38 | 38 |
| 40 #if $advanced_settings.sAdvanced == "Yes": | 40 #if $advanced_settings.sAdvanced == "Yes": |
| 41 #if str($advanced_settings.library_type) != 'auto': | 41 #if str($advanced_settings.library_type) != 'auto': |
| 42 --library-type=$advanced_settings.library_type | 42 --library-type=$advanced_settings.library_type |
| 43 #end if | 43 #end if |
| 44 #if $advanced_settings.mask_file: | 44 #if $advanced_settings.mask_file: |
| 45 --mask-file=$advanced_settings.mask_file | 45 --mask-file '$advanced_settings.mask_file' |
| 46 #end if | 46 #end if |
| 47 --max-mle-iterations=$advanced_settings.max_mle_iterations | 47 --max-mle-iterations=$advanced_settings.max_mle_iterations |
| 48 --max-bundle-frags=$advanced_settings.max_bundle_frags | 48 --max-bundle-frags=$advanced_settings.max_bundle_frags |
| 49 #end if | 49 #end if |
| 50 ## Inputs. | 50 ## Inputs. |
| 51 $gtf_input | 51 '$gtf_input' |
| 52 #set samplestring = ','.join( [ str( $sample.sample ) for $sample in $samples ] ) | 52 #set samplestring = ','.join( [ str( $sample.sample ) for $sample in $samples ] ) |
| 53 $samplestring | 53 '$samplestring' |
| 54 </command> | 54 </command> |
| 55 <inputs> | 55 <inputs> |
| 56 <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" | 56 <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" |
| 57 help="A transcript annotation (GFF3 or GTF) file produced by cufflinks, cuffcompare, or other source."/> | 57 help="A transcript annotation (GFF3 or GTF) file produced by cufflinks, cuffcompare, or other source."/> |
| 58 | 58 |