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comparison hicup_truncater.xml @ 5:30b199ed897d draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
author bgruening
date Sat, 22 Oct 2022 08:37:07 +0000
parents 17f80a8600ac
children cc413be789ea
comparison
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4:17f80a8600ac 5:30b199ed897d
1 <tool id="hicup_truncater" name="Hicup Truncater" version="@VERSION@.0"> 1 <tool id="hicup_truncater" name="Hicup Truncater" version="@VERSION@+galaxy0">
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 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 ##Dealing with fastq and fastq.gz 8 ##Dealing with inputs
9 #if $input_first_sequence.is_of_type("fastq.gz", "fastqsanger.gz"): 9 @PAIRED-END_INPUT@
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 10
17 #if $input_second_sequence.is_of_type("fastq.gz", "fastqsanger.gz"): 11 hicup_truncater --re1 '$re1' --zip $advanced_options.nofill
18 ln -s $input_second_sequence dataset2.gz && 12 '$read1'
19 #set input2='dataset2.gz' 13 '$read2'
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
26 #if $advanced_options.sequences:
27 --sequences '$advanced_options.sequences'
28 #end if
29 $input1 $input2
30 ]]></command> 14 ]]></command>
31 <inputs> 15 <inputs>
32 <expand macro="input_files" /> 16 <expand macro="input_paired"/>
33 <expand macro="re1" /> 17 <expand macro="re1"/>
34 <section name="advanced_options" title="Advanced options"> 18 <section name="advanced_options" title="Advanced options">
35 <expand macro="no_fill" /> 19 <expand macro="no_fill"/>
36 <param argument="--sequences" type="text" value="" label="Ligation sequence" help="Instead of specifying a restriction enzyme recognition sequence, specify the ligation sequences directly"/>
37 </section> 20 </section>
38 </inputs> 21 </inputs>
39 <outputs> 22 <outputs>
40 <data name="hicup_truncater_summary" format="txt" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary*.txt" /> 23 <data name="dataset1_trunc" format="fastq.gz" label="Hicup Truncation on ${on_string}: Read 1 Output" from_work_dir="dataset1*.trunc.fastq.gz">
41 <data name="dataset1_trunc" format="fastq.gz" label="Hicup Dataset1 Truncation" from_work_dir="dataset1*.trunc.fastq.gz" /> 24 <filter>library['type'] != 'paired_collection'</filter>
42 <data name="dataset2_trunc" format="fastq.gz" label="Hicup Dataset2 Truncation" from_work_dir="dataset2*.trunc.fastq.gz" /> 25 </data>
43 <data name="dataset1_truncater_barchart" format="svg" label="Hicup Dataset1 Truncation Barchart.svg" from_work_dir="dataset1*.truncation_barchart.svg" /> 26 <data name="dataset2_trunc" format="fastq.gz" label="Hicup Truncation on ${on_string}: Read 2 Output" from_work_dir="dataset2*.trunc.fastq.gz">
44 <data name="dataset2_truncater_barchart" format="svg" label="Hicup Dataset2 Truncation Barchart.svg" from_work_dir="dataset2*.truncation_barchart.svg" /> 27 <filter>library['type'] != 'paired_collection'</filter>
28 </data>
29 <collection name="dataset_trunc_pairs" type="paired" format="fastq.gz" label="Hicup Truncation on ${on_string}">
30 <filter>library['type'] == 'paired_collection' and 'multiple_output' not in output_selector</filter>
31 <data name="forward" from_work_dir="dataset1*.trunc.fastq.gz"/>
32 <data name="reverse" from_work_dir="dataset2*.trunc.fastq.gz"/>
33 </collection>
34 <data name="hicup_truncater_summary" format="tabular" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary*.txt"/>
35 <collection type="list" name="truncation_barchart" label="Truncation Barchart.svg">
36 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.truncation_barchart\.svg$" directory="./" ext="svg"/>
37 </collection>
45 </outputs> 38 </outputs>
46 <tests> 39 <tests>
47 <test> 40 <test>
48 <param name="input_first_sequence" value="dataset1.fastq" ftype="fastq"/> 41 <conditional name="library">
49 <param name="input_second_sequence" value="dataset2.fastq" ftype="fastq"/> 42 <param name="type" value="paired"/>
43 <param name="input_1" value="dataset1.fastq" ftype="fastq"/>
44 <param name="input_2" value="dataset2.fastq" ftype="fastq"/>
45 </conditional>
50 <param name="re1" value="A^AGCTT"/> 46 <param name="re1" value="A^AGCTT"/>
51 47 <output name="hicup_truncater_summary">
52 <output name="hicup_truncater_summary" file="hicup_truncater_summary.txt" lines_diff="8"/> 48 <assert_contents>
53 <output name="dataset1_trunc" file="dataset1.trunc.fastq.gz" compare="sim_size"/> 49 <has_text_matching expression="\s+99742\s+7230\s+7.25\s+92512\s+92.75\s+22.45"/>
54 <output name="dataset2_trunc" file="dataset2.trunc.fastq.gz" compare="sim_size"/> 50 <has_text_matching expression="\s+99742\s+7114\s+7.13\s+92628\s+92.87\s+22.63"/>
55 <output name="dataset1_truncater_barchart" file="dataset1.truncation_barchart.svg" ftype="svg" lines_diff="1000" /> 51 </assert_contents>
56 <output name="dataset2_truncater_barchart" file="dataset2.truncation_barchart.svg" ftype="svg" lines_diff="1000" /> 52 </output>
53 <output name="dataset1_trunc" file="dataset1.trunc.fastq.gz" decompress="true"/>
54 <output name="dataset2_trunc" file="dataset2.trunc.fastq.gz" decompress="true"/>
55 <output_collection name="truncation_barchart" count="2">
56 <element name="dataset1.fq" file="dataset1.truncation_barchart.svg" ftype="svg" compare="sim_size"/>
57 <element name="dataset2.fq" file="dataset2.truncation_barchart.svg" ftype="svg" compare="sim_size"/>
58 </output_collection>
59 </test>
60 <test>
61 <conditional name="library">
62 <param name="type" value="paired_collection"/>
63 <param name="input_1">
64 <collection type="paired">
65 <element name="forward" ftype="fastq" value="dataset1.fastq"/>
66 <element name="reverse" ftype="fastq" value="dataset2.fastq"/>
67 </collection>
68 </param>
69 </conditional>
70 <param name="re1" value="A^AGCTT"/>
71 <output name="hicup_truncater_summary">
72 <assert_contents>
73 <has_text_matching expression="\s+99742\s+7230\s+7.25\s+92512\s+92.75\s+22.45"/>
74 <has_text_matching expression="\s+99742\s+7114\s+7.13\s+92628\s+92.87\s+22.63"/>
75 </assert_contents>
76 </output>
77 <output_collection name="dataset_trunc_pairs" type="paired" count="2">
78 <element name="forward" decompress="true" file="dataset1.trunc.fastq.gz" ftype="fastq.gz"/>
79 <element name="reverse" decompress="true" file="dataset2.trunc.fastq.gz" ftype="fastq.gz"/>
80 </output_collection>
81 <output_collection name="truncation_barchart" count="2">
82 <element name="dataset1.fq" file="dataset1.truncation_barchart.svg" ftype="svg" compare="sim_size"/>
83 <element name="dataset2.fq" file="dataset2.truncation_barchart.svg" ftype="svg" compare="sim_size"/>
84 </output_collection>
57 </test> 85 </test>
58 </tests> 86 </tests>
59 <help><![CDATA[ 87 <help><![CDATA[
60 88
61 For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/ 89 For help please consult the documentation of HiCUP: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html
62 90
63 To get more information about the truncater visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Truncater 91 To get more information about the truncater visit: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html#hicup-truncater
64 ]]></help> 92 ]]></help>
65 93 <expand macro="citation_hicup"/>
66 <expand macro="citation_hicup" />
67 </tool> 94 </tool>