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comparison stringtie_merge.xml @ 12:f70601406e0e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
author iuc
date Mon, 18 Jul 2016 06:53:19 -0400
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11:52f55ad3dee2 12:f70601406e0e
1 <tool id="stringtie_merge" name="StringTie" version="0.1.0">
2 <description>merge transcripts</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <expand macro="version_command" />
9 <command>
10 <![CDATA[
11 stringtie --merge
12 -p \${GALAXY_SLOTS:-1}
13 #if str($guide_gff) != "":
14 -G "$guide_gff"
15 #end if
16 -m $min_len
17 -c $min_cov
18 -F $min_fpkm
19 -T $min_tpm
20 -f $min_iso
21 -g $gap_len
22 $keep_introns
23 #set inputs = '" "'.join(str($input_gtf).split(','))
24 -o $out_gtf "$inputs"
25 ]]>
26 </command>
27 <inputs>
28 <param type="data" name="input_gtf" multiple="true" format="gtf,gff3" />
29 <param type="data" name="guide_gff" optional="True" format="gtf,gff3" />
30 <param argument="-m" type="integer" name="min_len" value="50" help="Minimum input transcript length to include in the merge" />
31 <param argument="-c" type="integer" name="min_cov" value="0" help="Minimum input transcript coverage to include in the merge" />
32 <param argument="-F" type="float" name="min_fpkm" value="1.0" help="Minimum input transcript FPKM to include in the merge" />
33 <param argument="-T" type="float" name="min_tpm" value="1.0" help="Minimum input transcript TPM to include in the merge" />
34 <param argument="-f" type="float" name="min_iso" value="0.01" help="Minimum isoform fraction" />
35 <param argument="-g" type="integer" name="gap_len" value="250" help="Gap between transcripts to merge together" />
36 <param argument="-i" type="boolean" truevalue="-i" falsevalue="" name="keep_introns" help="Keep merged transcripts with retained introns" />
37 </inputs>
38 <outputs>
39 <data name="out_gtf" format="gtf" />
40 </outputs>
41 <tests>
42 <test>
43 <param ftype="gtf" name="input_gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf" />
44 <param ftype="gtf" name="guide_gff" value="stringtie_in.gtf" />
45 <output file="stringtie_merge_out1.gtf" ftype="gtf" lines_diff="2" name="out_gtf" />
46 </test>
47 <test>
48 <param ftype="gtf" name="input_gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
49 <param ftype="gtf" name="guide_gff" value="stringtie_merge_in3.gtf" />
50 <output file="stringtie_merge_out2.gtf" ftype="gtf" lines_diff="2" name="out_gtf" />
51 </test>
52 </tests>
53 <help><![CDATA[
54
55 **What it does?**
56
57 This is a special usage mode of StringTie_, distinct from the assembly usage mode. In the merge mode, StringTie takes as input a list of GTF/GFF files and merges/assembles these transcripts into a non-redundant set of transcripts. This mode is used in the new differential analysis pipeline to generate a global, unified set of transcripts (isoforms) across multiple RNA-Seq samples.
58
59 If a reference annotation is provided, StringTie will assemble the transfrags from the input GTF files with the reference transcripts.
60
61 .. _StringTie: http://ccb.jhu.edu/software/stringtie/
62
63 ------
64
65 StringTie --merge has the following options::
66
67 -G <guide_gff> reference annotation to include in the merging (GTF/GFF3)
68 -o <out_gtf> output file name for the merged transcripts GTF
69 (default: stdout)
70 -m <min_len> minimum input transcript length to include in the merge
71 (default: 50)
72 -c <min_cov> minimum input transcript coverage to include in the merge
73 (default: 0)
74 -F <min_fpkm> minimum input transcript FPKM to include in the merge
75 (default: 1.0)
76 -T <min_tpm> minimum input transcript TPM to include in the merge
77 (default: 1.0)
78 -f <min_iso> minimum isoform fraction (default: 0.01)
79 -g <gap_len> gap between transcripts to merge together (default: 250)
80 -i keep merged transcripts with retained introns; by default
81 these are not kept unless there is strong evidence for them
82 -l <label> name prefix for output transcripts (default: MSTRG)
83 ]]></help>
84 <expand macro="citations" />
85 </tool>