Mercurial > repos > bgruening > hicup_truncater

comparison hicup_truncater.xml @ 4:17f80a8600ac draft

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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
author bgruening
date Fri, 25 May 2018 17:50:43 -0400
parents e525d4f051b9
children 30b199ed897d
comparison
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3:7e21a0b8d48c 4:17f80a8600ac
2 <description>terminates sequence reads at specified Hi-C ligation junctions.</description> 2 <description>terminates sequence reads at specified Hi-C ligation junctions.</description>
3 <macros> 3 <macros>
4 <import>hicup_macros.xml</import> 4 <import>hicup_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements_hicup" /> 6 <expand macro="requirements_hicup" />
7 <expand macro="stdio" /> 7 <command detect_errors="exit_code"><![CDATA[
8 <command><![CDATA[ 8 ##Dealing with fastq and fastq.gz
9 hicup_truncater --re1 '$re1' $advanced_options.nofill 9 #if $input_first_sequence.is_of_type("fastq.gz", "fastqsanger.gz"):
10 ln -s $input_first_sequence dataset1.gz &&
11 #set input1='dataset1.gz'
12 #else
13 ln -s $input_first_sequence dataset1 &&
14 #set input1='dataset1'
15 #end if
16
17 #if $input_second_sequence.is_of_type("fastq.gz", "fastqsanger.gz"):
18 ln -s $input_second_sequence dataset2.gz &&
19 #set input2='dataset2.gz'
20 #else
21 ln -s $input_second_sequence dataset2 &&
22 #set input2='dataset2'
23 #end if
24
25 hicup_truncater --zip --re1 '$re1' $advanced_options.nofill
10 #if $advanced_options.sequences: 26 #if $advanced_options.sequences:
11 --sequences '$advanced_options.sequences' 27 --sequences '$advanced_options.sequences'
12 #end if 28 #end if
13 '$input_first_sequence' '$input_second_sequence' 29 $input1 $input2
14
15 && mv hicup_truncater_summary* hicup_truncater_summary.txt
16 && trunc_result_1=\$(echo '$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> 30 ]]></command>
25 <inputs> 31 <inputs>
26 <expand macro="input_files" /> 32 <expand macro="input_files" />
27 <expand macro="re1" /> 33 <expand macro="re1" />
28 <section name="advanced_options" title="Advanced options"> 34 <section name="advanced_options" title="Advanced options">
29 <expand macro="no_fill" /> 35 <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"/> 36 <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> 37 </section>
32 </inputs> 38 </inputs>
33 <outputs> 39 <outputs>
34 <expand macro="truncater_output" /> 40 <data name="hicup_truncater_summary" format="txt" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary*.txt" />
35 41 <data name="dataset1_trunc" format="fastq.gz" label="Hicup Dataset1 Truncation" from_work_dir="dataset1*.trunc.fastq.gz" />
42 <data name="dataset2_trunc" format="fastq.gz" label="Hicup Dataset2 Truncation" from_work_dir="dataset2*.trunc.fastq.gz" />
43 <data name="dataset1_truncater_barchart" format="svg" label="Hicup Dataset1 Truncation Barchart.svg" from_work_dir="dataset1*.truncation_barchart.svg" />
44 <data name="dataset2_truncater_barchart" format="svg" label="Hicup Dataset2 Truncation Barchart.svg" from_work_dir="dataset2*.truncation_barchart.svg" />
36 </outputs> 45 </outputs>
37 <tests> 46 <tests>
38 <test> 47 <test>
39 <param name="input_first_sequence" value="dataset1.fastq" ftype="fastq"/> 48 <param name="input_first_sequence" value="dataset1.fastq" ftype="fastq"/>
40 <param name="input_second_sequence" value="dataset2.fastq" ftype="fastq"/> 49 <param name="input_second_sequence" value="dataset2.fastq" ftype="fastq"/>
41 <param name="re1" value="A^AGCTT"/> 50 <param name="re1" value="A^AGCTT"/>
42 51
43 <output name="hicup_truncater_summary" file="hicup_truncater_summary.txt" lines_diff="8"/> 52 <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" /> 53 <output name="dataset1_trunc" file="dataset1.trunc.fastq.gz" compare="sim_size"/>
45 <output name="dataset2_trunc" file="dataset2.trunc.fastq" lines_diff="8"/> 54 <output name="dataset2_trunc" file="dataset2.trunc.fastq.gz" compare="sim_size"/>
46 <output name="dataset1_truncater_barchart" file="dataset1.truncation_barchart.svg" ftype="svg" lines_diff="1000" /> 55 <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" /> 56 <output name="dataset2_truncater_barchart" file="dataset2.truncation_barchart.svg" ftype="svg" lines_diff="1000" />
48 </test> 57 </test>
49 </tests> 58 </tests>
50 <help><![CDATA[ 59 <help><![CDATA[