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comparison stringtie_merge.xml @ 23:8eb8750070d4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 252f4cccd66513c985b3df9480d73c8b9f994520
author iuc
date Tue, 30 Apr 2024 11:53:08 +0000
parents ae618321f34a
children cbf488da3b2c
comparison
equal deleted inserted replaced
22:ae618321f34a 23:8eb8750070d4
1 <tool id="stringtie_merge" name="StringTie merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="stringtie_merge" name="StringTie merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>transcripts</description> 2 <description>transcripts</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
3 <xrefs> 6 <xrefs>
4 <xref type="bio.tools">stringtie</xref> 7 <xref type="bio.tools">stringtie</xref>
5 </xrefs> 8 </xrefs>
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9 <expand macro="requirements" /> 9 <expand macro="requirements" />
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 <expand macro="version_command" /> 11 <expand macro="version_command" />
12 <command><![CDATA[ 12 <command><![CDATA[
13 stringtie --merge 13 stringtie --merge
24 $keep_introns 24 $keep_introns
25 #set inputs = "' '".join(str($input_gtf).split(',')) 25 #set inputs = "' '".join(str($input_gtf).split(','))
26 -o '$out_gtf' '$inputs' 26 -o '$out_gtf' '$inputs'
27 ]]></command> 27 ]]></command>
28 <inputs> 28 <inputs>
29 <param name="input_gtf" type="data" format="gtf,gff3" multiple="true" label="Transcripts" help="In GTF or GFF3 format" /> 29 <param name="input_gtf" type="data" format="gtf,gff3" multiple="true" label="Transcripts" help="In GTF or GFF3 format"/>
30 <param name="guide_gff" argument="-G" type="data" format="gtf,gff3" optional="true" label="Reference annotation to include in the merging" /> 30 <param name="guide_gff" argument="-G" type="data" format="gtf,gff3" optional="true" label="Reference annotation to include in the merging"/>
31 <param name="min_len" argument="-m" type="integer" min="0" value="50" label="Minimum input transcript length to include in the merge" /> 31 <param name="min_len" argument="-m" type="integer" min="0" value="50" label="Minimum input transcript length to include in the merge"/>
32 <param name="min_cov" argument="-c" type="integer" min="0" value="0" label="Minimum input transcript coverage to include in the merge" /> 32 <param name="min_cov" argument="-c" type="integer" min="0" value="0" label="Minimum input transcript coverage to include in the merge"/>
33 <param name="min_fpkm" argument="-F" type="float" min="0" value="1" label="Minimum input transcript FPKM to include in the merge" /> 33 <param name="min_fpkm" argument="-F" type="float" min="0" value="1" label="Minimum input transcript FPKM to include in the merge"/>
34 <param name="min_tpm" argument="-T" type="float" min="0" value="1" label="Minimum input transcript TPM to include in the merge" /> 34 <param name="min_tpm" argument="-T" type="float" min="0" value="1" label="Minimum input transcript TPM to include in the merge"/>
35 <param name="min_iso" argument="-f" type="float" value="0.01" label="Minimum isoform fraction" /> 35 <param name="min_iso" argument="-f" type="float" value="0.01" label="Minimum isoform fraction"/>
36 <param name="gap_len" argument="-g" type="integer" value="250" label="Gap between transcripts to merge together" /> 36 <param name="gap_len" argument="-g" type="integer" value="250" label="Gap between transcripts to merge together"/>
37 <param name="keep_introns" argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Keep merged transcripts with retained introns" help="By default these are not kept unless there is strong evidence for them" /> 37 <param name="keep_introns" argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Keep merged transcripts with retained introns" help="By default these are not kept unless there is strong evidence for them"/>
38 </inputs> 38 </inputs>
39 <outputs> 39 <outputs>
40 <data name="out_gtf" format="gtf" /> 40 <data name="out_gtf" format="gtf"/>
41 </outputs> 41 </outputs>
42 <tests> 42 <tests>
43 <test> 43 <test>
44 <param name="input_gtf" ftype="gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf" /> 44 <param name="input_gtf" ftype="gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf"/>
45 <param name="guide_gff" ftype="gtf" value="stringtie_in.gtf" /> 45 <param name="guide_gff" ftype="gtf" value="stringtie_in.gtf"/>
46 <output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" compare="re_match" sort="true"/> 46 <output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" lines_diff="2"/>
47 </test> 47 </test>
48 <test> 48 <test>
49 <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" /> 49 <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf"/>
50 <param name="guide_gff" ftype="gtf" value="stringtie_merge_in3.gtf" /> 50 <param name="guide_gff" ftype="gtf" value="stringtie_merge_in3.gtf" />
51 <output name="out_gtf" file="stringtie_merge_out2.gtf" ftype="gtf" compare="re_match" sort="true"/> 51 <output name="out_gtf" file="stringtie_merge_out2.gtf" ftype="gtf" lines_diff="4"/>
52 </test> 52 </test>
53 <test> 53 <test>
54 <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" /> 54 <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf"/>
55 <output name="out_gtf" ftype="gtf"> 55 <output name="out_gtf" ftype="gtf">
56 <assert_contents> 56 <assert_contents>
57 <has_text text="stringtie --merge" /> 57 <has_text text="stringtie --merge"/>
58 </assert_contents> 58 </assert_contents>
59 </output> 59 </output>
60 </test> 60 </test>
61 </tests> 61 </tests>
62 <help><![CDATA[ 62 <help><![CDATA[