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comparison sicer_wrapper.xml @ 3:ddebd5f4338b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 4d5b98367b51a9e2f2711d1ccea9753a415d973a
author devteam
date Wed, 24 Oct 2018 11:30:33 -0400
parents 61e1ccffd3fa
children
comparison
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2:937bb12c0f5c 3:ddebd5f4338b
1 <tool id="peakcalling_sicer" name="SICER" version="0.0.1"> 1 <tool id="peakcalling_sicer" name="SICER" version="0.0.2">
2 <description>Statistical approach for the Identification of ChIP-Enriched Regions</description> 2 <description>Statistical approach for the Identification of ChIP-Enriched Regions</description>
3 <command interpreter="python">sicer_wrapper.py 3 <command interpreter="python">sicer_wrapper.py
4 --bed_file '${input_bed_file}' 4 --bed_file '${input_bed_file}'
5 #if str( $input_control_file ) != 'None': 5 #if str( $input_control_file ) != 'None':
6 --control_file '${input_control_file}' 6 --control_file '${input_control_file}'
76 <param name="window_size" value="200" /> 76 <param name="window_size" value="200" />
77 <param name="fragment_size" value="150" /> 77 <param name="fragment_size" value="150" />
78 <param name="effective_genome_fraction" value="0.74" /> 78 <param name="effective_genome_fraction" value="0.74" />
79 <param name="gap_size" value="600" /> 79 <param name="gap_size" value="600" />
80 <param name="error_cut_off" value="0.01" /> 80 <param name="error_cut_off" value="0.01" />
81 <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_1/test-1-removed.bed" /> 81 <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
82 <output name="summary_graph_output_file" file="peakcalling_sicer/test_1/test-W200.graph" /> 82 <output name="summary_graph_output_file" file="test_1_test-W200.graph" />
83 <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-normalized.wig" /> 83 <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
84 <output name="island_filtered_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed" /> 84 <output name="island_filtered_output_file" file="test-W200-G600-E0.01-islandfiltered.bed" />
85 <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig" /> 85 <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-E0.01-islandfiltered-normalized.wig" />
86 <output name="score_island_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01.scoreisland" /> 86 <output name="score_island_output_file" file="test_1_test-W200-G600-E0.01.scoreisland" />
87 <output name="output_log_file" file="peakcalling_sicer/test_1/output_log_file.contains" compare="contains"/> 87 <output name="output_log_file" file="test_1_output_log_file.contains" compare="contains"/>
88 </test> 88 </test>
89 <test> 89 <test>
90 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" /> 90 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
91 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" /> 91 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" />
92 <param name="fix_off_by_one_errors" /> 92 <param name="fix_off_by_one_errors" />
94 <param name="window_size" value="200" /> 94 <param name="window_size" value="200" />
95 <param name="fragment_size" value="150" /> 95 <param name="fragment_size" value="150" />
96 <param name="effective_genome_fraction" value="0.74" /> 96 <param name="effective_genome_fraction" value="0.74" />
97 <param name="gap_size" value="600" /> 97 <param name="gap_size" value="600" />
98 <param name="error_cut_off" value="0.01" /> 98 <param name="error_cut_off" value="0.01" />
99 <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_2/test-1-removed.bed" /> 99 <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
100 <output name="redundancy_removed_control_bed_output_file" file="peakcalling_sicer/test_2/control-1-removed.bed" /> 100 <output name="redundancy_removed_control_bed_output_file" file="control-1-removed.bed" />
101 <output name="summary_graph_output_file" file="peakcalling_sicer/test_2/test-W200.graph" /> 101 <output name="summary_graph_output_file" file="test_1_test-W200.graph" />
102 <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-normalized.wig" /> 102 <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
103 <output name="significant_islands_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-island.bed" /> 103 <output name="significant_islands_output_file" file="test_2_test-W200-G600-FDR0.01-island.bed" />
104 <output name="island_filtered_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed" /> 104 <output name="island_filtered_output_file" file="test-W200-G600-FDR0.01-islandfiltered.bed" />
105 <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig" /> 105 <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />
106 <output name="score_island_output_file" file="peakcalling_sicer/test_2/test-W200-G600.scoreisland" /> 106 <output name="score_island_output_file" file="test_2_test-W200-G600.scoreisland" />
107 <output name="islands_summary_output_file" file="peakcalling_sicer/test_2/test-W200-G600-islands-summary" /> 107 <output name="islands_summary_output_file" file="test_2_test-W200-G600-islands-summary" />
108 <output name="significant_islands_summary_output_file" file="peakcalling_sicer/test_2/test-W200-G600-islands-summary-FDR0.01" /> 108 <output name="significant_islands_summary_output_file" file="test_2_test-W200-G600-islands-summary-FDR0.01" />
109 <output name="output_log_file" file="peakcalling_sicer/test_2/output_log_file.contains" compare="contains"/> 109 <output name="output_log_file" file="test_2_output_log_file.contains" compare="contains"/>
110 </test> 110 </test>
111 <test> 111 <test>
112 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" /> 112 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
113 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" /> 113 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" />
114 <param name="fix_off_by_one_errors" value="True" /> 114 <param name="fix_off_by_one_errors" value="True" />
116 <param name="window_size" value="200" /> 116 <param name="window_size" value="200" />
117 <param name="fragment_size" value="150" /> 117 <param name="fragment_size" value="150" />
118 <param name="effective_genome_fraction" value="0.74" /> 118 <param name="effective_genome_fraction" value="0.74" />
119 <param name="gap_size" value="600" /> 119 <param name="gap_size" value="600" />
120 <param name="error_cut_off" value="0.01" /> 120 <param name="error_cut_off" value="0.01" />
121 <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_2/test-1-removed.bed" /> 121 <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
122 <output name="redundancy_removed_control_bed_output_file" file="peakcalling_sicer/test_2/control-1-removed.bed" /> 122 <output name="redundancy_removed_control_bed_output_file" file="control-1-removed.bed" />
123 <output name="summary_graph_output_file" file="peakcalling_sicer/test_3/test-W200.graph" /> 123 <output name="summary_graph_output_file" file="test_3_test-W200.graph" />
124 <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-normalized.wig" /> 124 <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
125 <output name="significant_islands_output_file" file="peakcalling_sicer/test_3/test-W200-G600-FDR0.01-island.bed" /> 125 <output name="significant_islands_output_file" file="test_3_test-W200-G600-FDR0.01-island.bed" />
126 <output name="island_filtered_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed" /> 126 <output name="island_filtered_output_file" file="test-W200-G600-FDR0.01-islandfiltered.bed" />
127 <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig" /> 127 <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />
128 <output name="score_island_output_file" file="peakcalling_sicer/test_3/test-W200-G600.scoreisland" /> 128 <output name="score_island_output_file" file="test_3_test-W200-G600.scoreisland" />
129 <output name="islands_summary_output_file" file="peakcalling_sicer/test_3/test-W200-G600-islands-summary" /> 129 <output name="islands_summary_output_file" file="test_3_test-W200-G600-islands-summary" />
130 <output name="significant_islands_summary_output_file" file="peakcalling_sicer/test_3/test-W200-G600-islands-summary-FDR0.01" /> 130 <output name="significant_islands_summary_output_file" file="test_3_test-W200-G600-islands-summary-FDR0.01" />
131 <output name="output_log_file" file="peakcalling_sicer/test_2/output_log_file.contains" compare="contains"/> 131 <output name="output_log_file" file="test_2_output_log_file.contains" compare="contains"/>
132 </test> 132 </test>
133 <test> 133 <test>
134 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" /> 134 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
135 <param name="input_control_file" /> 135 <param name="input_control_file" />
136 <param name="fix_off_by_one_errors" value="True" /> 136 <param name="fix_off_by_one_errors" value="True" />
138 <param name="window_size" value="200" /> 138 <param name="window_size" value="200" />
139 <param name="fragment_size" value="150" /> 139 <param name="fragment_size" value="150" />
140 <param name="effective_genome_fraction" value="0.74" /> 140 <param name="effective_genome_fraction" value="0.74" />
141 <param name="gap_size" value="600" /> 141 <param name="gap_size" value="600" />
142 <param name="error_cut_off" value="0.01" /> 142 <param name="error_cut_off" value="0.01" />
143 <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_1/test-1-removed.bed" /> 143 <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
144 <output name="summary_graph_output_file" file="peakcalling_sicer/test_4/test-W200.graph" /> 144 <output name="summary_graph_output_file" file="test_3_test-W200.graph" />
145 <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-normalized.wig" /> 145 <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
146 <output name="island_filtered_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed" /> 146 <output name="island_filtered_output_file" file="test-W200-G600-E0.01-islandfiltered.bed" />
147 <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig" /> 147 <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-E0.01-islandfiltered-normalized.wig" />
148 <output name="score_island_output_file" file="peakcalling_sicer/test_4/test-W200-G600-E0.01.scoreisland" /> 148 <output name="score_island_output_file" file="test_4_test-W200-G600-E0.01.scoreisland" />
149 <output name="output_log_file" file="peakcalling_sicer/test_1/output_log_file.contains" compare="contains"/> 149 <output name="output_log_file" file="test_1_output_log_file.contains" compare="contains"/>
150 </test> 150 </test>
151 </tests> 151 </tests>
152 <help> 152 <help>
153 **What it does** 153 **What it does**
154 154