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comparison hicstuff_pipeline.xml @ 3:7ffc3748ffde draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff commit 685c4b08d3001bdce6bd33cee10804e6c312d5b9
author iuc
date Mon, 25 Nov 2024 10:33:09 +0000
parents 7beecdd0976f
children
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2:7beecdd0976f 3:7ffc3748ffde
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@">0</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'
11 --outdir results 11 --outdir results
12 --aligner $aligner 12 --aligner $aligner
77 <data name="fragments_list" from_work_dir="./results/fragments_list.txt" format="tabular" label="${tool.name} on ${on_string}: Fragment list"/> 77 <data name="fragments_list" from_work_dir="./results/fragments_list.txt" format="tabular" label="${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 ${on_string}: Contig info"/> 78 <data name="info_contigs" from_work_dir="./results/info_contigs.txt" format="tabular" label="${tool.name} on ${on_string}: Contig info"/>
79 </outputs> 79 </outputs>
80 <tests> 80 <tests>
81 <test expect_num_outputs="3"> 81 <test expect_num_outputs="3">
82 <param name="genome" value="seq.fa.gz" /> 82 <param name="genome" value="seq.fa.gz"/>
83 <param name="paired_cond|paired_select" value="separate"/> 83 <param name="paired_cond|paired_select" value="separate"/>
84 <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"/>
85 <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"> 86 <output name="abs_fragments_contacts_weighted_graal">
87 <assert_contents> 87 <assert_contents>
88 <has_n_lines n="77"/> 88 <has_n_lines n="77"/>
89 <has_n_columns n="3"/> 89 <has_n_columns n="3"/>
90 </assert_contents> 90 </assert_contents>
95 <has_n_columns n="6"/> 95 <has_n_columns n="6"/>
96 </assert_contents> 96 </assert_contents>
97 </output> 97 </output>
98 <output name="info_contigs" file="info_contigs.txt"/> 98 <output name="info_contigs" file="info_contigs.txt"/>
99 <assert_stderr> 99 <assert_stderr>
100 <has_text text="Contact map generated" /> 100 <has_text text="Contact map generated"/>
101 </assert_stderr> 101 </assert_stderr>
102 </test> 102 </test>
103 <!-- bg2 format --> 103 <!-- bg2 format -->
104 <test expect_num_outputs="3"> 104 <test expect_num_outputs="3">
105 <param name="genome" value="seq.fa.gz" /> 105 <param name="genome" value="seq.fa.gz"/>
106 <param name="paired_cond|paired_select" value="separate"/> 106 <param name="paired_cond|paired_select" value="separate"/>
107 <param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz" /> 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" /> 108 <param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz"/>
109 <param name="matfmt" value="bg2"/> 109 <param name="matfmt" value="bg2"/>
110 <output name="abs_fragments_contacts_weighted_bg2"> 110 <output name="abs_fragments_contacts_weighted_bg2">
111 <assert_contents> 111 <assert_contents>
112 <has_n_lines n="76"/> 112 <has_n_lines n="76"/>
113 <has_n_columns n="7"/> 113 <has_n_columns n="7"/>
119 <has_n_columns n="6"/> 119 <has_n_columns n="6"/>
120 </assert_contents> 120 </assert_contents>
121 </output> 121 </output>
122 <output name="info_contigs" file="info_contigs.txt"/> 122 <output name="info_contigs" file="info_contigs.txt"/>
123 <assert_stderr> 123 <assert_stderr>
124 <has_text text="Contact map generated" /> 124 <has_text text="Contact map generated"/>
125 </assert_stderr> 125 </assert_stderr>
126 </test> 126 </test>
127 <!-- cool format --> 127 <!-- cool format -->
128 <test expect_num_outputs="3"> 128 <test expect_num_outputs="3">
129 <param name="genome" value="seq.fa.gz" /> 129 <param name="genome" value="seq.fa.gz"/>
130 <param name="paired_cond|paired_select" value="separate"/> 130 <param name="paired_cond|paired_select" value="separate"/>
131 <param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz" /> 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" /> 132 <param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz"/>
133 <param name="matfmt" value="cool"/> 133 <param name="matfmt" value="cool"/>
134 <output name="abs_fragments_contacts_weighted_cool"> 134 <output name="abs_fragments_contacts_weighted_cool">
135 <assert_contents> 135 <assert_contents>
136 <has_h5_keys keys="bins,chroms,indexes,pixels"/> 136 <has_h5_keys keys="bins,chroms,indexes,pixels"/>
137 </assert_contents> 137 </assert_contents>
142 <has_n_columns n="6"/> 142 <has_n_columns n="6"/>
143 </assert_contents> 143 </assert_contents>
144 </output> 144 </output>
145 <output name="info_contigs" file="info_contigs.txt"/> 145 <output name="info_contigs" file="info_contigs.txt"/>
146 <assert_stderr> 146 <assert_stderr>
147 <has_text text="Contact map generated" /> 147 <has_text text="Contact map generated"/>
148 </assert_stderr> 148 </assert_stderr>
149 </test> 149 </test>
150 </tests> 150 </tests>
151 <help><![CDATA[ 151 <help><![CDATA[
152 152
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. 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.
169 * Fragment ist: Contains genomic coordinates of the matrix bins (row/columns). 169 * Fragment ist: Contains genomic coordinates of the matrix bins (row/columns).
170 * Contig info.txt: Contains chromosome names, theirs length and number of bins. 170 * Contig info.txt: Contains chromosome names, theirs length and number of bins.
171 171
172 ]]></help> 172 ]]></help>
173 <expand macro="citations" /> 173 <expand macro="citations"/>
174 </tool> 174 </tool>