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comparison hicup_truncater.xml @ 0:f413e09ae289 draft

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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
author bgruening
date Thu, 09 Mar 2017 09:32:44 -0500
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children e525d4f051b9
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-1:000000000000 0:f413e09ae289
1 <tool id="hicup_truncater" name="Hicup Truncater" version="0.1.0">
2 <description>terminates sequence reads at specified Hi-C ligation junctions.</description>
3 <macros>
4 <import>hicup_macros.xml</import>
5 </macros>
6 <expand macro="requirements_hicup" />
7 <expand macro="stdio" />
8 <command><![CDATA[
9 hicup_truncater --re1 '$re1' $advanced_options.nofill
10 #if $advanced_options.sequences:
11 --sequences '$advanced_options.sequences'
12 #end if
13 '$input_first_sequence' '$input_second_sequence'
14
15 && mv hicup_truncater_summary* hicup_truncater_summary.txt
16 && trunc_result_1=\$(echo '$input_first_sequence' | rev | cut -d'/' -f1 | rev)
17
18 && mv \$trunc_result_1.trunc.fastq dataset1.trunc.fastq
19 && trunc_result_2=\$(echo '$input_second_sequence' | rev | cut -d'/' -f1 | rev)
20 && mv \$trunc_result_2.trunc.fastq dataset2.trunc.fastq
21 && mv \$trunc_result_1.truncation_barchart.svg dataset1.truncation_barchart.svg
22 && mv \$trunc_result_2.truncation_barchart.svg dataset2.truncation_barchart.svg
23
24 ]]></command>
25 <inputs>
26 <expand macro="input_files" />
27 <expand macro="re1" />
28 <section name="advanced_options" title="Advanced options">
29 <expand macro="no_fill" />
30 <param argument="--sequences" type="text" value="" label="Ligation sequence" help="Instead of specifying a restriction enzyme recognition sequence, specify the ligation sequences directly"/>
31 </section>
32 </inputs>
33 <outputs>
34 <expand macro="truncater_output" />
35
36 </outputs>
37 <tests>
38 <test>
39 <param name="input_first_sequence" value="dataset1.fastq" ftype="fastq"/>
40 <param name="input_second_sequence" value="dataset2.fastq" ftype="fastq"/>
41 <param name="re1" value="A^AGCTT"/>
42
43 <output name="hicup_truncater_summary" file="hicup_truncater_summary.txt" lines_diff="8"/>
44 <output name="dataset1_trunc" file="dataset1.trunc.fastq" lines_diff="8" />
45 <output name="dataset2_trunc" file="dataset2.trunc.fastq" lines_diff="8"/>
46 <output name="dataset1_truncater_barchart" file="dataset1.truncation_barchart.svg" ftype="svg" lines_diff="1000" />
47 <output name="dataset2_truncater_barchart" file="dataset2.truncation_barchart.svg" ftype="svg" lines_diff="1000" />
48 </test>
49 </tests>
50 <help><![CDATA[
51
52 For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/
53
54 To get more information about the truncater visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Truncater
55 ]]></help>
56
57 <expand macro="citation_hicup" />
58 </tool>