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annotate ccat_wrapper.xml @ 2:e0b378d6844f 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 16:27:17 +0000
parents bbfd1fbff28a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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2
e0b378d6844f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat commit 1370bb21ee5712a13a26d289065406c5d489b8cc"
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1 <tool id="peakcalling_ccat" name="CCAT" version="0.0.2" profile="20.01">
0
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2 <description>Control-based ChIP-seq Analysis Tool</description>
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3 <requirements>
2
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4 <requirement type="package" version="3.0">ccat</requirement>
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5 </requirements>
2
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6 <stdio>
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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;"
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8 source="both"
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9 level="fatal"
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10 description="CLI error" />
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11 <regex match="tag file error" source="both" level="fatal" description="tag file error" />
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12 </stdio>
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13 <command detect_errors="aggressive"><![CDATA[
e0b378d6844f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat commit 1370bb21ee5712a13a26d289065406c5d489b8cc"
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14 echo $in_test_mode && CCAT '$input_tag_file'
e0b378d6844f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat commit 1370bb21ee5712a13a26d289065406c5d489b8cc"
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15 '$input_control_file'
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16 #if str($in_test_mode) == "no":
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17 '$chromInfo'
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18 #else:
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19 '$__tool_directory__/test-data/genome_length_mm8_chr19.txt'
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20 #end if
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21 #if str($options_type['options_type_selector']) == 'advanced':
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22 '$input_advanced_config_file'
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23 #else:
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24 '${options_type.input_config_file.fields.path}'
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25 #end if
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26 CCAT
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27 | tee '$output_log_file'
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28 ]]></command>
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29 <configfiles>
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30 <configfile name="input_advanced_config_file"><![CDATA[
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31 #if str($options_type['options_type_selector']) == 'advanced':
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32 fragmentSize ${options_type['fragment_size']}
e0b378d6844f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat commit 1370bb21ee5712a13a26d289065406c5d489b8cc"
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33 slidingWinSize ${options_type['sliding_window_size']}
e0b378d6844f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat commit 1370bb21ee5712a13a26d289065406c5d489b8cc"
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34 movingStep ${options_type['moving_step']}
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35 isStrandSensitiveMode ${options_type['is_strand_sensitive_mode']}
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36 minCount ${options_type['min_count']}
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37 outputNum ${options_type['output_num']}
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38 randomSeed ${options_type['random_seed']}
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39 minScore ${options_type['min_score']}
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40 bootstrapPass ${options_type['bootstrap_pass']}
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41 #end if
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42 ]]></configfile>
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43 </configfiles>
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44 <inputs>
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45 <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File"/>
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46 <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File"/>
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47 <conditional name="options_type">
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48 <param name="options_type_selector" type="select" label="Advanced Options">
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49 <option value="basic" selected="True">Hide Advanced Options</option>
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50 <option value="advanced">Show Advanced Options</option>
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51 </param>
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52 <when value="basic">
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53 <param name="input_config_file" type="select" label="Select a pre-defined configuration file">
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54 <options from_data_table="ccat_configurations">
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55 <validator type="no_options" message="No configurations are available"/>
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56 </options>
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57 </param>
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58 </when>
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59 <when value="advanced">
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60 <param name="fragment_size" type="integer" label="Length of DNA fragment" value="200"/>
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61 <param name="sliding_window_size" type="integer" label="Sliding window size" value="500" help="transcription factor binding default: 300; histone modifications default: 500"/>
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62 <param name="moving_step" type="integer" label="Step of sliding window" value="50" help="transcription factor binding default: 10; histone modifications default: 50"/>
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63 <param name="is_strand_sensitive_mode" type="select" label="isStrandSensitiveMode" >
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64 <option value="1">Transition from sense strand to anti-sense strand</option>
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65 <option value="0" selected="True">Local maximum of read-enrichment profile</option>
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66 </param>
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67 <param name="min_count" type="integer" label="Minimum number of read counts at the peak" value="4"/>
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68 <param name="output_num" type="integer" label="Number of peaks reported in top peak file" value="100000"/>
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69 <param name="random_seed" type="integer" label="Random Seed" value="123456"/>
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70 <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/>
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71 <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/>
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72 </when>
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73 </conditional>
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74 <param name="in_test_mode" type="hidden" value="no" />
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75 </inputs>
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76 <outputs>
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77 <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)" from_work_dir="CCAT.significant.peak">
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78 <actions>
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79 <action type="metadata" name="chromCol" default="1"/>
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80 <action type="metadata" name="startCol" default="3"/>
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81 <action type="metadata" name="endCol" default="4"/>
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82 </actions>
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83 </data>
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84 <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)" from_work_dir="CCAT.significant.region">
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85 <actions>
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86 <action type="metadata" name="chromCol" default="1"/>
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87 <action type="metadata" name="startCol" default="3"/>
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88 <action type="metadata" name="endCol" default="4"/>
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89 </actions>
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90 </data>
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91 <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)" from_work_dir="CCAT.top100000.peak">
0
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92 <actions>
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93 <action type="metadata" name="chromCol" default="1"/>
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94 <action type="metadata" name="startCol" default="3"/>
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95 <action type="metadata" name="endCol" default="4"/>
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96 </actions>
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97 </data>
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98 <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/>
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99 </outputs>
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100 <tests>
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101 <test>
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102 <param name="input_tag_file" value="ES_CTCF_chr19.bed" ftype="bed" dbkey="hg18" />
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103 <param name="input_control_file" value="ES_GFP_chr19.bed" ftype="bed" dbkey="hg18" />
0
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104 <param name="options_type_selector" value="advanced" />
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105 <param name="fragment_size" value="200" />
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106 <param name="sliding_window_size" value="300" />
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107 <param name="moving_step" value="10" />
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108 <param name="is_strand_sensitive_mode" value="1" />
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109 <param name="min_count" value="3" />
0
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110 <param name="output_num" value="100000" />
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111 <param name="random_seed" value="123456" />
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112 <param name="min_score" value="5.0" />
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113 <param name="bootstrap_pass" value="50" />
2
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114 <param name="in_test_mode" value="yes" />
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115 <output name="output_peak_file" file="ES_CTCF_chr19.significant.peak"/>
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116 <output name="output_region_file" file="ES_CTCF_chr19.significant.region" />
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117 <output name="output_top_file" file="ES_CTCF_chr19.top100000.peak" />
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118 <output name="output_log_file" file="ES_CTCF_chr19.log" />
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119 </test>
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120 <test>
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121 <param name="input_tag_file" value="ES_CTCF_chr19.bed" ftype="bed" dbkey="hg18" />
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122 <param name="input_control_file" value="ES_GFP_chr19.bed" ftype="bed" dbkey="hg18" />
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123 <param name="options_type_selector" value="basic" />
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124 <param name="input_config_file" value="config_TF" />
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125 <param name="in_test_mode" value="yes" />
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126 <output name="output_peak_file" file="ES_CTCF_chr19.significant.peak" />
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127 <output name="output_region_file" file="ES_CTCF_chr19.significant.region" />
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128 <output name="output_top_file" file="ES_CTCF_chr19.top100000.peak" />
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129 <output name="output_log_file" file="ES_CTCF_chr19.log" />
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130 </test>
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131 </tests>
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132 <help>
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133 **What it does**
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134
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135 This tool allows ChIP-seq peak/region calling using CCAT.
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136
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137 View the original CCAT documentation: https://www.comp.nus.edu.sg/~bioinfo/CCAT3.0/
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138 </help>
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139 <citations>
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140 <citation type="doi">10.1093/bioinformatics/btq128</citation>
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141 </citations>
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142 </tool>