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comparison ccat_wrapper.xml @ 2:1a6979fbd544 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat commit 1370bb21ee5712a13a26d289065406c5d489b8cc"
author devteam
date Fri, 03 Dec 2021 16:27:57 +0000
parents 201d8e7dfc43
children
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1:201d8e7dfc43 2:1a6979fbd544
1 <tool id="peakcalling_ccat" name="CCAT" version="0.0.1"> 1 <tool id="peakcalling_ccat" name="CCAT" version="0.0.2" profile="20.01">
2 <description>Control-based ChIP-seq Analysis Tool</description> 2 <description>Control-based ChIP-seq Analysis Tool</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.0">CCAT</requirement> 4 <requirement type="package" version="3.0">ccat</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python">ccat_wrapper.py '$input_tag_file' '$input_control_file' '$chromInfo' 6 <stdio>
7 #if str( $options_type[ 'options_type_selector' ] ) == 'advanced': 7 <regex match="Usage: &lt;library 1 tag file name&gt; &lt;library 2 tag file name&gt; &lt;chromosome length file name&gt; &lt;config file name&gt; &lt;project name&gt;"
8 '$input_advanced_config_file' 8 source="both"
9 #else: 9 level="fatal"
10 '${ options_type.input_config_file.fields.path }' 10 description="CLI error" />
11 #end if 11 <regex match="tag file error" source="both" level="fatal" description="tag file error" />
12 'CCAT in Galaxy' 12 </stdio>
13 '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command> 13 <command detect_errors="aggressive"><![CDATA[
14 echo $in_test_mode && CCAT '$input_tag_file'
15 '$input_control_file'
16 #if str($in_test_mode) == "no":
17 '$chromInfo'
18 #else:
19 '$__tool_directory__/test-data/genome_length_mm8_chr19.txt'
20 #end if
21 #if str($options_type['options_type_selector']) == 'advanced':
22 '$input_advanced_config_file'
23 #else:
24 '${options_type.input_config_file.fields.path}'
25 #end if
26 CCAT
27 | tee '$output_log_file'
28 ]]></command>
29 <configfiles>
30 <configfile name="input_advanced_config_file"><![CDATA[
31 #if str($options_type['options_type_selector']) == 'advanced':
32 fragmentSize ${options_type['fragment_size']}
33 slidingWinSize ${options_type['sliding_window_size']}
34 movingStep ${options_type['moving_step']}
35 isStrandSensitiveMode ${options_type['is_strand_sensitive_mode']}
36 minCount ${options_type['min_count']}
37 outputNum ${options_type['output_num']}
38 randomSeed ${options_type['random_seed']}
39 minScore ${options_type['min_score']}
40 bootstrapPass ${options_type['bootstrap_pass']}
41 #end if
42 ]]></configfile>
43 </configfiles>
14 <inputs> 44 <inputs>
15 <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" > 45 <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File"/>
16 <validator type="unspecified_build" /> 46 <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File"/>
17 </param>
18 <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" >
19 <validator type="unspecified_build" />
20 </param>
21 <conditional name="options_type"> 47 <conditional name="options_type">
22 <param name="options_type_selector" type="select" label="Advanced Options"> 48 <param name="options_type_selector" type="select" label="Advanced Options">
23 <option value="basic" selected="True">Hide Advanced Options</option> 49 <option value="basic" selected="True">Hide Advanced Options</option>
24 <option value="advanced">Show Advanced Options</option> 50 <option value="advanced">Show Advanced Options</option>
25 </param> 51 </param>
43 <param name="random_seed" type="integer" label="Random Seed" value="123456"/> 69 <param name="random_seed" type="integer" label="Random Seed" value="123456"/>
44 <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/> 70 <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/>
45 <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/> 71 <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/>
46 </when> 72 </when>
47 </conditional> 73 </conditional>
74 <param name="in_test_mode" type="hidden" value="no" />
48 </inputs> 75 </inputs>
49 <outputs> 76 <outputs>
50 <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)"> 77 <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)" from_work_dir="CCAT.significant.peak">
51 <actions> 78 <actions>
52 <action type="metadata" name="chromCol" default="1"/> 79 <action type="metadata" name="chromCol" default="1"/>
53 <action type="metadata" name="startCol" default="3"/> 80 <action type="metadata" name="startCol" default="3"/>
54 <action type="metadata" name="endCol" default="4"/> 81 <action type="metadata" name="endCol" default="4"/>
55 </actions> 82 </actions>
56 </data> 83 </data>
57 <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)"> 84 <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)" from_work_dir="CCAT.significant.region">
58 <actions> 85 <actions>
59 <action type="metadata" name="chromCol" default="1"/> 86 <action type="metadata" name="chromCol" default="1"/>
60 <action type="metadata" name="startCol" default="3"/> 87 <action type="metadata" name="startCol" default="3"/>
61 <action type="metadata" name="endCol" default="4"/> 88 <action type="metadata" name="endCol" default="4"/>
62 </actions> 89 </actions>
63 </data> 90 </data>
64 <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)"> 91 <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)" from_work_dir="CCAT.top100000.peak">
65 <actions> 92 <actions>
66 <action type="metadata" name="chromCol" default="1"/> 93 <action type="metadata" name="chromCol" default="1"/>
67 <action type="metadata" name="startCol" default="3"/> 94 <action type="metadata" name="startCol" default="3"/>
68 <action type="metadata" name="endCol" default="4"/> 95 <action type="metadata" name="endCol" default="4"/>
69 </actions> 96 </actions>
70 </data> 97 </data>
71 <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/> 98 <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/>
72 </outputs> 99 </outputs>
73 <configfiles>
74 <configfile name="input_advanced_config_file">#if str( $options_type['options_type_selector' ] ) == 'advanced':
75 fragmentSize ${options_type[ 'fragment_size' ]}
76 slidingWinSize ${options_type[ 'sliding_window_size' ]}
77 movingStep ${options_type[ 'moving_step' ]}
78 isStrandSensitiveMode ${options_type[ 'is_strand_sensitive_mode' ]}
79 minCount ${options_type[ 'min_count' ]}
80 outputNum ${options_type[ 'output_num' ]}
81 randomSeed ${options_type[ 'random_seed' ]}
82 minScore ${options_type[ 'min_score' ]}
83 bootstrapPass ${options_type[ 'bootstrap_pass' ]}
84 #end if</configfile>
85 </configfiles>
86 <tests> 100 <tests>
87 <test> 101 <test>
88 <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> 102 <param name="input_tag_file" value="ES_CTCF_chr19.bed" ftype="bed" dbkey="hg18" />
89 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> 103 <param name="input_control_file" value="ES_GFP_chr19.bed" ftype="bed" dbkey="hg18" />
90 <param name="options_type_selector" value="advanced" /> 104 <param name="options_type_selector" value="advanced" />
91 <param name="fragment_size" value="200" /> 105 <param name="fragment_size" value="200" />
92 <param name="sliding_window_size" value="500" /> 106 <param name="sliding_window_size" value="300" />
93 <param name="moving_step" value="50" /> 107 <param name="moving_step" value="10" />
94 <param name="is_strand_sensitive_mode" value="0" /> 108 <param name="is_strand_sensitive_mode" value="1" />
95 <param name="min_count" value="4" /> 109 <param name="min_count" value="3" />
96 <param name="output_num" value="100000" /> 110 <param name="output_num" value="100000" />
97 <param name="random_seed" value="123456" /> 111 <param name="random_seed" value="123456" />
98 <param name="min_score" value="5.0" /> 112 <param name="min_score" value="5.0" />
99 <param name="bootstrap_pass" value="50" /> 113 <param name="bootstrap_pass" value="50" />
100 <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" /> 114 <param name="in_test_mode" value="yes" />
101 <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" /> 115 <output name="output_peak_file" file="ES_CTCF_chr19.significant.peak"/>
102 <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="True" /> 116 <output name="output_region_file" file="ES_CTCF_chr19.significant.region" />
103 <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" /> 117 <output name="output_top_file" file="ES_CTCF_chr19.top100000.peak" />
118 <output name="output_log_file" file="ES_CTCF_chr19.log" />
104 </test> 119 </test>
105 <test> 120 <test>
106 <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> 121 <param name="input_tag_file" value="ES_CTCF_chr19.bed" ftype="bed" dbkey="hg18" />
107 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> 122 <param name="input_control_file" value="ES_GFP_chr19.bed" ftype="bed" dbkey="hg18" />
108 <param name="options_type_selector" value="basic" /> 123 <param name="options_type_selector" value="basic" />
109 <param name="input_config_file" value="ccat_3.0_histone_config" /> 124 <param name="input_config_file" value="config_TF" />
110 <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" /> 125 <param name="in_test_mode" value="yes" />
111 <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" /> 126 <output name="output_peak_file" file="ES_CTCF_chr19.significant.peak" />
112 <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="true" /> 127 <output name="output_region_file" file="ES_CTCF_chr19.significant.region" />
113 <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" /> 128 <output name="output_top_file" file="ES_CTCF_chr19.top100000.peak" />
129 <output name="output_log_file" file="ES_CTCF_chr19.log" />
114 </test> 130 </test>
115 <!-- Test below gives different answers on different architectures,
116 e.g.: x86_64 GNU/Linux gave an extra line (additional peak called) when compared to the version running on 10.6.0 Darwin i386
117 slidingWinSize was fixed to be 1000, default as per readme.txt
118 -->
119 <!--
120 <test>
121 <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />
122 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />
123 <param name="options_type_selector" value="basic" />
124 <param name="input_config_file" value="ccat_3.0_histone_config_readme" />
125 <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_2.interval.re_match" compare="re_match" />
126 <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match" compare="re_match" />
127 <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_2.interval.sorted.re_match" compare="re_match" sort="true" />
128 <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_2.txt" />
129 </test>
130 -->
131 </tests> 131 </tests>
132 <help> 132 <help>
133 **What it does** 133 **What it does**
134 134
135 This tool allows ChIP-seq peak/region calling using CCAT. 135 This tool allows ChIP-seq peak/region calling using CCAT.
136 136
137 View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm. 137 View the original CCAT documentation: https://www.comp.nus.edu.sg/~bioinfo/CCAT3.0/
138
139 ------
140
141 **Citation**
142
143 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
144
145 </help> 138 </help>
146 <citations> 139 <citations>
147 <citation type="doi">10.1093/bioinformatics/btq128</citation> 140 <citation type="doi">10.1093/bioinformatics/btq128</citation>
148 </citations> 141 </citations>
149 </tool> 142 </tool>