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comparison stringtie_merge.xml @ 11:6e45b443ef1f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf
author iuc
date Thu, 01 Jun 2017 12:16:04 -0400
parents c84d44519b2e
children dd4df992d93d
comparison
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10:c84d44519b2e 11:6e45b443ef1f
1 <tool id="stringtie_merge" name="StringTie" version="1.3.3"> 1 <tool id="stringtie_merge" name="StringTie merge" version="1.3.3">
2 <description>merge transcripts</description> 2 <description>transcripts</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 <command> 9 <command><![CDATA[
10 <![CDATA[
11 stringtie --merge 10 stringtie --merge
12 -p \${GALAXY_SLOTS:-1} 11 -p \${GALAXY_SLOTS:-1}
13 #if $guide_gff: 12 #if $guide_gff:
14 -G "$guide_gff" 13 -G '$guide_gff'
15 #end if 14 #end if
16 -m $min_len 15 -m $min_len
17 -c $min_cov 16 -c $min_cov
18 -F $min_fpkm 17 -F $min_fpkm
19 -T $min_tpm 18 -T $min_tpm
20 -f $min_iso 19 -f $min_iso
21 -g $gap_len 20 -g $gap_len
22 $keep_introns 21 $keep_introns
23 #set inputs = '" "'.join(str($input_gtf).split(',')) 22 #set inputs = "' '".join(str($input_gtf).split(','))
24 -o $out_gtf "$inputs" 23 -o '$out_gtf' '$inputs'
25 ]]> 24 ]]></command>
26 </command>
27 <inputs> 25 <inputs>
28 <param type="data" name="input_gtf" multiple="True" format="gtf,gff3" /> 26 <param name="input_gtf" type="data" format="gtf,gff3" multiple="true" label="Transcripts" help="In GTF or GFF3 format" />
29 <param type="data" name="guide_gff" optional="True" format="gtf,gff3" /> 27 <param name="guide_gff" argument="-G" type="data" format="gtf,gff3" optional="true" label="Reference annotation to include in the merging" />
30 <param argument="-m" type="integer" name="min_len" value="50" help="Minimum input transcript length to include in the merge" /> 28 <param name="min_len" argument="-m" type="integer" value="50" label="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" /> 29 <param name="min_cov" argument="-c" type="integer" value="0" label="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" /> 30 <param name="min_fpkm" argument="-F" type="float" value="1.0" label="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" /> 31 <param name="min_tpm" argument="-T" type="float" value="1.0" label="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" /> 32 <param name="min_iso" argument="-f" type="float" value="0.01" label="Minimum isoform fraction" />
35 <param argument="-g" type="integer" name="gap_len" value="250" help="Gap between transcripts to merge together" /> 33 <param name="gap_len" argument="-g" type="integer" value="250" label="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" /> 34 <param name="keep_introns" argument="-i" type="boolean" truevalue="-i" falsevalue="" label="Keep merged transcripts with retained introns" help="By default these are not kept unless there is strong evidence for them" />
37 </inputs> 35 </inputs>
38 <outputs> 36 <outputs>
39 <data name="out_gtf" format="gtf" /> 37 <data name="out_gtf" format="gtf" />
40 </outputs> 38 </outputs>
41 <tests> 39 <tests>
42 <test> 40 <test>
43 <param ftype="gtf" name="input_gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf" /> 41 <param name="input_gtf" ftype="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" /> 42 <param name="guide_gff" ftype="gtf" value="stringtie_in.gtf" />
45 <output file="stringtie_merge_out1.gtf" ftype="gtf" lines_diff="2" name="out_gtf" /> 43 <output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" lines_diff="2" />
46 </test> 44 </test>
47 <test> 45 <test>
48 <param ftype="gtf" name="input_gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" /> 46 <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
49 <param ftype="gtf" name="guide_gff" value="stringtie_merge_in3.gtf" /> 47 <param name="guide_gff" ftype="gtf" value="stringtie_merge_in3.gtf" />
50 <output file="stringtie_merge_out2.gtf" ftype="gtf" lines_diff="2" name="out_gtf" /> 48 <output name="out_gtf" file="stringtie_merge_out2.gtf" ftype="gtf" lines_diff="2" />
51 </test> 49 </test>
52 <test> 50 <test>
53 <param ftype="gtf" name="input_gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" /> 51 <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
54 <output ftype="gtf" name="out_gtf"> 52 <output name="out_gtf" ftype="gtf">
55 <assert_contents> 53 <assert_contents>
56 <has_text text="stringtie --merge" /> 54 <has_text text="stringtie --merge" />
57 </assert_contents> 55 </assert_contents>
58 </output> 56 </output>
59 </test> 57 </test>
60 </tests> 58 </tests>
61 <help><![CDATA[ 59 <help><![CDATA[
62
63 **What it does?** 60 **What it does?**
64 61
65 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. 62 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.
66 63
67 If a reference annotation is provided, StringTie will assemble the transfrags from the input GTF files with the reference transcripts. 64 If a reference annotation is provided, StringTie will assemble the transfrags from the input GTF files with the reference transcripts.
68 65
69 .. _StringTie: http://ccb.jhu.edu/software/stringtie/ 66 .. _StringTie: http://ccb.jhu.edu/software/stringtie/
70
71 ------
72
73 StringTie --merge has the following options::
74
75 -G <guide_gff> reference annotation to include in the merging (GTF/GFF3)
76 -o <out_gtf> output file name for the merged transcripts GTF
77 (default: stdout)
78 -m <min_len> minimum input transcript length to include in the merge
79 (default: 50)
80 -c <min_cov> minimum input transcript coverage to include in the merge
81 (default: 0)
82 -F <min_fpkm> minimum input transcript FPKM to include in the merge
83 (default: 1.0)
84 -T <min_tpm> minimum input transcript TPM to include in the merge
85 (default: 1.0)
86 -f <min_iso> minimum isoform fraction (default: 0.01)
87 -g <gap_len> gap between transcripts to merge together (default: 250)
88 -i keep merged transcripts with retained introns; by default
89 these are not kept unless there is strong evidence for them
90 -l <label> name prefix for output transcripts (default: MSTRG)
91 ]]></help> 67 ]]></help>
92 <expand macro="citations" /> 68 <expand macro="citations" />
93 </tool> 69 </tool>