Mercurial > repos > devteam > ccat
annotate ccat_wrapper.xml @ 1:201d8e7dfc43 draft
planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
| author | devteam |
|---|---|
| date | Tue, 21 Jul 2015 14:13:34 -0400 |
| parents | a0c8dc671a23 |
| children | 1a6979fbd544 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="peakcalling_ccat" name="CCAT" version="0.0.1"> |
| 2 <description>Control-based ChIP-seq Analysis Tool</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="3.0">CCAT</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python">ccat_wrapper.py '$input_tag_file' '$input_control_file' '$chromInfo' | |
| 7 #if str( $options_type[ 'options_type_selector' ] ) == 'advanced': | |
| 8 '$input_advanced_config_file' | |
| 9 #else: | |
| 10 '${ options_type.input_config_file.fields.path }' | |
| 11 #end if | |
| 12 'CCAT in Galaxy' | |
| 13 '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command> | |
| 14 <inputs> | |
| 15 <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" > | |
| 16 <validator type="unspecified_build" /> | |
| 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"> | |
| 22 <param name="options_type_selector" type="select" label="Advanced Options"> | |
| 23 <option value="basic" selected="True">Hide Advanced Options</option> | |
| 24 <option value="advanced">Show Advanced Options</option> | |
| 25 </param> | |
| 26 <when value="basic"> | |
| 27 <param name="input_config_file" type="select" label="Select a pre-defined configuration file"> | |
| 28 <options from_data_table="ccat_configurations"> | |
| 29 <validator type="no_options" message="No configurations are available"/> | |
| 30 </options> | |
| 31 </param> | |
| 32 </when> | |
| 33 <when value="advanced"> | |
| 34 <param name="fragment_size" type="integer" label="Length of DNA fragment" value="200"/> | |
| 35 <param name="sliding_window_size" type="integer" label="Sliding window size" value="500" help="transcription factor binding default: 300; histone modifications default: 500"/> | |
| 36 <param name="moving_step" type="integer" label="Step of sliding window" value="50" help="transcription factor binding default: 10; histone modifications default: 50"/> | |
| 37 <param name="is_strand_sensitive_mode" type="select" label="isStrandSensitiveMode" > | |
| 38 <option value="1">Transition from sense strand to anti-sense strand</option> | |
| 39 <option value="0" selected="True">Local maximum of read-enrichment profile</option> | |
| 40 </param> | |
| 41 <param name="min_count" type="integer" label="Minimum number of read counts at the peak" value="4"/> | |
| 42 <param name="output_num" type="integer" label="Number of peaks reported in top peak file" value="100000"/> | |
| 43 <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"/> | |
| 45 <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/> | |
| 46 </when> | |
| 47 </conditional> | |
| 48 </inputs> | |
| 49 <outputs> | |
| 50 <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)"> | |
| 51 <actions> | |
| 52 <action type="metadata" name="chromCol" default="1"/> | |
| 53 <action type="metadata" name="startCol" default="3"/> | |
| 54 <action type="metadata" name="endCol" default="4"/> | |
| 55 </actions> | |
| 56 </data> | |
| 57 <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)"> | |
| 58 <actions> | |
| 59 <action type="metadata" name="chromCol" default="1"/> | |
| 60 <action type="metadata" name="startCol" default="3"/> | |
| 61 <action type="metadata" name="endCol" default="4"/> | |
| 62 </actions> | |
| 63 </data> | |
| 64 <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)"> | |
| 65 <actions> | |
| 66 <action type="metadata" name="chromCol" default="1"/> | |
| 67 <action type="metadata" name="startCol" default="3"/> | |
| 68 <action type="metadata" name="endCol" default="4"/> | |
| 69 </actions> | |
| 70 </data> | |
| 71 <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/> | |
| 72 </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> | |
| 87 <test> | |
| 88 <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> | |
| 89 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> | |
| 90 <param name="options_type_selector" value="advanced" /> | |
| 91 <param name="fragment_size" value="200" /> | |
| 92 <param name="sliding_window_size" value="500" /> | |
| 93 <param name="moving_step" value="50" /> | |
| 94 <param name="is_strand_sensitive_mode" value="0" /> | |
| 95 <param name="min_count" value="4" /> | |
| 96 <param name="output_num" value="100000" /> | |
| 97 <param name="random_seed" value="123456" /> | |
| 98 <param name="min_score" value="5.0" /> | |
| 99 <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" /> | |
| 101 <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" /> | |
| 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" /> | |
| 103 <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" /> | |
| 104 </test> | |
| 105 <test> | |
| 106 <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> | |
| 107 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> | |
| 108 <param name="options_type_selector" value="basic" /> | |
| 109 <param name="input_config_file" value="ccat_3.0_histone_config" /> | |
| 110 <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" /> | |
| 111 <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" /> | |
| 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" /> | |
| 113 <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" /> | |
| 114 </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> | |
| 132 <help> | |
| 133 **What it does** | |
| 134 | |
| 135 This tool allows ChIP-seq peak/region calling using CCAT. | |
| 136 | |
| 137 View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm. | |
| 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> | |
|
1
201d8e7dfc43
planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
0
diff
changeset
|
146 <citations> |
|
201d8e7dfc43
planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
0
diff
changeset
|
147 <citation type="doi">10.1093/bioinformatics/btq128</citation> |
|
201d8e7dfc43
planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
0
diff
changeset
|
148 </citations> |
| 0 | 149 </tool> |