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comparison cuffquant_wrapper.xml @ 2:b2ee2bef1926 draft

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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
comparison
equal deleted inserted replaced
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>&amp;1 | head -n 1</version_command> 9 <version_command>cuffquant 2>&amp;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