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comparison cuffmerge_wrapper.xml @ 12:1707a530e598 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
author devteam
date Tue, 07 Feb 2017 18:39:42 -0500
parents b6e3849293b1
children cf747d1bd79a
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11:8160c8ea4eb9 12:1707a530e598
1 <tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.0"> 1 <tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.0">
2 <description>merge together several Cufflinks assemblies</description> 2 <description>merge together several Cufflinks assemblies</description>
3 <expand macro="requirements" />
4 <expand macro="stdio" />
5 <macros> 3 <macros>
6 <import>cuff_macros.xml</import> 4 <import>cuff_macros.xml</import>
7 </macros> 5 </macros>
8 <command interpreter="python"> 6 <expand macro="requirements" />
9 cuffmerge_wrapper.py 7 <expand macro="stdio" />
8 <command>
9 python '$__tool_directory__/cuffmerge_wrapper.py'
10 --num-threads="\${GALAXY_SLOTS:-4}" 10 --num-threads="\${GALAXY_SLOTS:-4}"
11 11
12 ## Use annotation reference? 12 ## Use annotation reference?
13 #if $annotation.use_ref_annotation == "Yes": 13 #if $annotation.use_ref_annotation == "Yes":
14 -g "${annotation.reference_annotation}" 14 -g '${annotation.reference_annotation}'
15 #end if 15 #end if
16 16
17 ## Use sequence data? 17 ## Use sequence data?
18 #if $seq_data.use_seq_data == "Yes": 18 #if $seq_data.use_seq_data == "Yes":
19 -s 19 -s
20 #if $seq_data.seq_source.index_source == "history": 20 #if $seq_data.seq_source.index_source == "history":
21 --ref_file="${seq_data.seq_source.ref_file}" 21 --ref_file '${seq_data.seq_source.ref_file}'
22 #else: 22 #else:
23 --index="${seq_data.seq_source.index.fields.path}" 23 --index '${seq_data.seq_source.index.fields.path}'
24 #end if 24 #end if
25 #end if 25 #end if
26 26
27 --min-isoform-fraction="${min_isoform_fraction}" 27 --min-isoform-fraction="${min_isoform_fraction}"
28 28
29 ## Outputs. 29 ## Outputs.
30 --merged-transcripts="${merged_transcripts}" 30 --merged-transcripts '${merged_transcripts}'
31 31
32 @CUFFLINKS_GTF_INPUTS@ 32 @CUFFLINKS_GTF_INPUTS@
33 </command> 33 </command>
34 <inputs> 34 <inputs>
35 <expand macro="cufflinks_gtf_inputs" /> 35 <expand macro="cufflinks_gtf_inputs" />