Mercurial > repos > devteam > cuffmerge
comparison cuffmerge_wrapper.xml @ 14:6a6717a5f421 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
author | iuc |
---|---|
date | Tue, 16 Jun 2020 13:00:53 -0400 |
parents | cf747d1bd79a |
children | 86285ddd4512 |
comparison
equal
deleted
inserted
replaced
13:cf747d1bd79a | 14:6a6717a5f421 |
---|---|
1 <tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.1"> | 1 <tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.2"> |
2 <description>merge together several Cufflinks assemblies</description> | 2 <description>merge together several Cufflinks assemblies</description> |
3 <macros> | 3 <macros> |
4 <import>cuff_macros.xml</import> | 4 <import>cuff_macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
7 <version_command>cuffmerge -v</version_command> | 7 <version_command>cuffmerge -v</version_command> |
8 <command detect_errors="aggressive"> | 8 <command detect_errors="aggressive"><![CDATA[ |
9 python '$__tool_directory__/cuffmerge_wrapper.py' | 9 @CUFFLINKS_LINK_GTF_INPUTS@ |
10 echo @CUFFLINKS_GTF_INPUTS@ | sed 's/\s\+/\n/' > assembly_GTF_list.txt && | |
11 cuffmerge | |
12 -o output | |
10 --num-threads="\${GALAXY_SLOTS:-4}" | 13 --num-threads="\${GALAXY_SLOTS:-4}" |
11 | |
12 ## Use annotation reference? | 14 ## Use annotation reference? |
13 #if $annotation.use_ref_annotation == "Yes": | 15 #if $annotation.use_ref_annotation == "Yes": |
14 -g '${annotation.reference_annotation}' | 16 -g '${annotation.reference_annotation}' |
15 #end if | 17 #end if |
16 | 18 |
23 --index '${seq_data.seq_source.index.fields.path}' | 25 --index '${seq_data.seq_source.index.fields.path}' |
24 #end if | 26 #end if |
25 #end if | 27 #end if |
26 | 28 |
27 --min-isoform-fraction="${min_isoform_fraction}" | 29 --min-isoform-fraction="${min_isoform_fraction}" |
28 | 30 assembly_GTF_list.txt |
29 ## Outputs. | 31 ]]></command> |
30 --merged-transcripts '${merged_transcripts}' | |
31 | |
32 @CUFFLINKS_GTF_INPUTS@ | |
33 </command> | |
34 <inputs> | 32 <inputs> |
35 <expand macro="cufflinks_gtf_inputs" /> | 33 <expand macro="cufflinks_gtf_inputs" /> |
36 <conditional name="annotation"> | 34 <conditional name="annotation"> |
37 <param name="use_ref_annotation" type="select" label="Use Reference Annotation"> | 35 <param name="use_ref_annotation" type="select" label="Use Reference Annotation"> |
38 <option value="No">No</option> | 36 <option value="No">No</option> |
72 </conditional> | 70 </conditional> |
73 <param name="min_isoform_fraction" type="float" min="0" max="1" value="0.05" label="Minimum isoform fraction" help="Discard isoforms with abundance below this value" /> | 71 <param name="min_isoform_fraction" type="float" min="0" max="1" value="0.05" label="Minimum isoform fraction" help="Discard isoforms with abundance below this value" /> |
74 </inputs> | 72 </inputs> |
75 | 73 |
76 <outputs> | 74 <outputs> |
77 <data format="gtf" name="merged_transcripts" label="${tool.name} on ${on_string}: merged transcripts"/> | 75 <data format="gtf" name="merged_transcripts" label="${tool.name} on ${on_string}: merged transcripts" from_work_dir="output/merged.gtf"/> |
78 </outputs> | 76 </outputs> |
79 | 77 |
80 <tests> | 78 <tests> |
81 <!-- | 79 <!-- |
82 cuffmerge -g cuffcompare_in3.gtf cuffcompare_in1.gtf cuffcompare_in2.gtf | 80 cuffmerge -g cuffcompare_in3.gtf cuffcompare_in1.gtf cuffcompare_in2.gtf |
125 | 123 |
126 Merged transcripts file: | 124 Merged transcripts file: |
127 | 125 |
128 Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies. | 126 Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies. |
129 </help> | 127 </help> |
130 <citations> | 128 <expand macro="citations"/> |
131 <citation type="doi">10.1038/nbt.1621</citation> | |
132 </citations> | |
133 </tool> | 129 </tool> |