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comparison hicstuff_pipeline.xml @ 1:6956f0783d77 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff commit c1b3c8d3e6a2f18ae89918e89d8dc8a3a0a6d24c
author iuc
date Fri, 04 Oct 2024 08:48:01 +0000
parents 1efd17d2bfdb
children 7beecdd0976f
comparison
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0:1efd17d2bfdb 1:6956f0783d77
1 <tool id="hicstuff_pipeline" name="hicstuff full pipeline" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="hicstuff_pipeline" name="hicstuff full pipeline" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>generates a Hi-C contact matrix</description> 2 <description>generates a Hi-C contact matrix</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 hicstuff pipeline 9 hicstuff pipeline
10 --genome '$genome' 10 --genome '$genome'
16 $filter 16 $filter
17 --mapping $mapping 17 --mapping $mapping
18 --matfmt $matfmt 18 --matfmt $matfmt
19 --quality-min $quality_min 19 --quality-min $quality_min
20 --size $size 20 --size $size
21 --threads \${GALAXY_SLOTS:-1} 21 --threads "\${GALAXY_SLOTS:-1}"
22 #if $paired_cond.paired_select == "paired" 22 #if $paired_cond.paired_select == "paired"
23 '$paired_cond.reads.forward' 23 '$paired_cond.reads.forward'
24 '$paired_cond.reads.reverse' 24 '$paired_cond.reads.reverse'
25 #else 25 #else
26 '$forward_reads' 26 '$forward_reads'
63 </param> 63 </param>
64 <param argument="--quality-min" type="integer" value="30" label="Minimum mapping quality for selecting contacts"/> 64 <param argument="--quality-min" type="integer" value="30" label="Minimum mapping quality for selecting contacts"/>
65 <param argument="--size" type="integer" value="0" label="Minimum size threshold to consider contigs. Keep all contigs by default."/> 65 <param argument="--size" type="integer" value="0" label="Minimum size threshold to consider contigs. Keep all contigs by default."/>
66 </inputs> 66 </inputs>
67 <outputs> 67 <outputs>
68 <data name="abs_fragments_contacts_weighted" from_work_dir="./results/abs_fragments_contacts_weighter.txt" format="tabular"/> 68 <data name="abs_fragments_contacts_weighted_graal" from_work_dir="./results/abs_fragments_contacts_weighted.txt" format="tabular" label="${tool.name} on ${on_string}: Contact matrix (graal)">
69 <data name="fragments_list" from_work_dir="./results/fragments_list.txt" format="tabular"/> 69 <filter>matfmt == "graal"</filter>
70 <data name="info_contigs" from_work_dir="./results/info_contigs.txt" format="tabular"/> 70 </data>
71 <data name="abs_fragments_contacts_weighted_bg2" from_work_dir="./results/abs_fragments_contacts_weighted.bg2" format="tabular" label="${tool.name} on ${on_string}: Contact matrix (bg2)">
72 <filter>matfmt == "bg2"</filter>
73 </data>
74 <data name="abs_fragments_contacts_weighted_cool" from_work_dir="./results/abs_fragments_contacts_weighted.cool" format="cool" label="${tool.name} on ${on_string}: Contact matrix (cool)">
75 <filter>matfmt == "cool"</filter>
76 </data>
77 <data name="fragments_list" from_work_dir="./results/fragments_list.txt" format="tabular" label="${tool.name} on ${on_string}: Fragment list"/>
78 <data name="info_contigs" from_work_dir="./results/info_contigs.txt" format="tabular" label="${tool.name} on ${on_string}: Contig info"/>
71 </outputs> 79 </outputs>
72 <tests> 80 <tests>
73 <test> 81 <test expect_num_outputs="3">
74 <param name="genome" value="seq.fa.gz" /> 82 <param name="genome" value="seq.fa.gz" />
75 <param name="paired_cond|paired_select" value="separate"/> 83 <param name="paired_cond|paired_select" value="separate"/>
76 <param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz" /> 84 <param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz" />
77 <param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz" /> 85 <param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz" />
86 <output name="abs_fragments_contacts_weighted_graal">
87 <assert_contents>
88 <has_n_lines n="77"/>
89 <has_n_columns n="3"/>
90 </assert_contents>
91 </output>
92 <output name="fragments_list">
93 <assert_contents>
94 <has_n_lines n="17"/>
95 <has_n_columns n="6"/>
96 </assert_contents>
97 </output>
98 <output name="info_contigs" file="info_contigs.txt"/>
99 <assert_stderr>
100 <has_text text="Contact map generated" />
101 </assert_stderr>
102 </test>
103 <!-- bg2 format -->
104 <test expect_num_outputs="3">
105 <param name="genome" value="seq.fa.gz" />
106 <param name="paired_cond|paired_select" value="separate"/>
107 <param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz" />
108 <param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz" />
109 <param name="matfmt" value="bg2"/>
110 <output name="abs_fragments_contacts_weighted_bg2">
111 <assert_contents>
112 <has_n_lines n="76"/>
113 <has_n_columns n="7"/>
114 </assert_contents>
115 </output>
116 <output name="fragments_list">
117 <assert_contents>
118 <has_n_lines n="17"/>
119 <has_n_columns n="6"/>
120 </assert_contents>
121 </output>
122 <output name="info_contigs" file="info_contigs.txt"/>
123 <assert_stderr>
124 <has_text text="Contact map generated" />
125 </assert_stderr>
126 </test>
127 <!-- cool format -->
128 <test expect_num_outputs="3">
129 <param name="genome" value="seq.fa.gz" />
130 <param name="paired_cond|paired_select" value="separate"/>
131 <param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz" />
132 <param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz" />
133 <param name="matfmt" value="cool"/>
134 <output name="abs_fragments_contacts_weighted_cool">
135 <assert_contents>
136 <has_h5_keys keys="bins,chroms,indexes,pixels"/>
137 </assert_contents>
138 </output>
139 <output name="fragments_list">
140 <assert_contents>
141 <has_n_lines n="17"/>
142 <has_n_columns n="6"/>
143 </assert_contents>
144 </output>
78 <output name="info_contigs" file="info_contigs.txt"/> 145 <output name="info_contigs" file="info_contigs.txt"/>
79 <assert_stderr> 146 <assert_stderr>
80 <has_text text="Contact map generated" /> 147 <has_text text="Contact map generated" />
81 </assert_stderr> 148 </assert_stderr>
82 </test> 149 </test>
96 * reverse reads 163 * reverse reads
97 164
98 ------------ 165 ------------
99 Output files 166 Output files
100 ------------ 167 ------------
101 * abs_fragments_contacts_weighter.txt: Sparse matrix file with 3 columns the rows, column and values of nonzero pixels. The first row contains the shape and total number of nonzero pixels in the matrix. 168 * Contact matrix: Sparse matrix file with 3 columns the rows, column and values of nonzero pixels. The first row contains the shape and total number of nonzero pixels in the matrix.
102 * fragments_list.txt: Contains genomic coordinates of the matrix bins (row/columns). 169 * Fragment ist: Contains genomic coordinates of the matrix bins (row/columns).
103 * info_contigs.txt: Contains chromosome names, theirs length and number of bins. 170 * Contig info.txt: Contains chromosome names, theirs length and number of bins.
104 171
105 ]]></help> 172 ]]></help>
106 <expand macro="citations" /> 173 <expand macro="citations" />
107 </tool> 174 </tool>