comparison sicer_wrapper.xml @ 2:74c9214cc8e6 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 4d5b98367b51a9e2f2711d1ccea9753a415d973a

1:4a14714649b4

<tool id="peakcalling_sicer" name="SICER" version="0.0.1">
  <description>Statistical approach for the Identification of ChIP-Enriched Regions</description>
  <command interpreter="python">sicer_wrapper.py 
  --bed_file '${input_bed_file}' 
  #if str( $input_control_file ) != 'None':
      --control_file '${input_control_file}'

      <param name="window_size" value="200" />
      <param name="fragment_size" value="150" />
      <param name="effective_genome_fraction" value="0.74" />
      <param name="gap_size" value="600" />
      <param name="error_cut_off" value="0.01" />
      <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_1/test-1-removed.bed" />
      <output name="summary_graph_output_file" file="peakcalling_sicer/test_1/test-W200.graph" />
      <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-normalized.wig" />
      <output name="island_filtered_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed" />
      <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig" />
      <output name="score_island_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01.scoreisland" />
      <output name="output_log_file" file="peakcalling_sicer/test_1/output_log_file.contains" compare="contains"/>
    </test>
    <test>
      <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
      <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" />
      <param name="fix_off_by_one_errors" />

      <param name="window_size" value="200" />
      <param name="fragment_size" value="150" />
      <param name="effective_genome_fraction" value="0.74" />
      <param name="gap_size" value="600" />
      <param name="error_cut_off" value="0.01" />
      <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_2/test-1-removed.bed" />
      <output name="redundancy_removed_control_bed_output_file" file="peakcalling_sicer/test_2/control-1-removed.bed" />
      <output name="summary_graph_output_file" file="peakcalling_sicer/test_2/test-W200.graph" />
      <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-normalized.wig" />
      <output name="significant_islands_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-island.bed" />
      <output name="island_filtered_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed" />
      <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />
      <output name="score_island_output_file" file="peakcalling_sicer/test_2/test-W200-G600.scoreisland" />
      <output name="islands_summary_output_file" file="peakcalling_sicer/test_2/test-W200-G600-islands-summary" />
      <output name="significant_islands_summary_output_file" file="peakcalling_sicer/test_2/test-W200-G600-islands-summary-FDR0.01" />
      <output name="output_log_file" file="peakcalling_sicer/test_2/output_log_file.contains" compare="contains"/>
    </test>
    <test>
      <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
      <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" />
      <param name="fix_off_by_one_errors" value="True" />

      <param name="window_size" value="200" />
      <param name="fragment_size" value="150" />
      <param name="effective_genome_fraction" value="0.74" />
      <param name="gap_size" value="600" />
      <param name="error_cut_off" value="0.01" />
      <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_2/test-1-removed.bed" />
      <output name="redundancy_removed_control_bed_output_file" file="peakcalling_sicer/test_2/control-1-removed.bed" />
      <output name="summary_graph_output_file" file="peakcalling_sicer/test_3/test-W200.graph" />
      <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-normalized.wig" />
      <output name="significant_islands_output_file" file="peakcalling_sicer/test_3/test-W200-G600-FDR0.01-island.bed" />
      <output name="island_filtered_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed" />
      <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />
      <output name="score_island_output_file" file="peakcalling_sicer/test_3/test-W200-G600.scoreisland" />
      <output name="islands_summary_output_file" file="peakcalling_sicer/test_3/test-W200-G600-islands-summary" />
      <output name="significant_islands_summary_output_file" file="peakcalling_sicer/test_3/test-W200-G600-islands-summary-FDR0.01" />
      <output name="output_log_file" file="peakcalling_sicer/test_2/output_log_file.contains" compare="contains"/>
    </test>
    <test>
      <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
      <param name="input_control_file" />
      <param name="fix_off_by_one_errors" value="True" />

      <param name="window_size" value="200" />
      <param name="fragment_size" value="150" />
      <param name="effective_genome_fraction" value="0.74" />
      <param name="gap_size" value="600" />
      <param name="error_cut_off" value="0.01" />
      <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_1/test-1-removed.bed" />
      <output name="summary_graph_output_file" file="peakcalling_sicer/test_4/test-W200.graph" />
      <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-normalized.wig" />
      <output name="island_filtered_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed" />
      <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig" />
      <output name="score_island_output_file" file="peakcalling_sicer/test_4/test-W200-G600-E0.01.scoreisland" />
      <output name="output_log_file" file="peakcalling_sicer/test_1/output_log_file.contains" compare="contains"/>
    </test>
  </tests>
  <help>
**What it does**

2:74c9214cc8e6

<tool id="peakcalling_sicer" name="SICER" version="0.0.2">
  <description>Statistical approach for the Identification of ChIP-Enriched Regions</description>
  <command interpreter="python">sicer_wrapper.py 
  --bed_file '${input_bed_file}' 
  #if str( $input_control_file ) != 'None':
      --control_file '${input_control_file}'

      <param name="window_size" value="200" />
      <param name="fragment_size" value="150" />
      <param name="effective_genome_fraction" value="0.74" />
      <param name="gap_size" value="600" />
      <param name="error_cut_off" value="0.01" />
      <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
      <output name="summary_graph_output_file" file="test_1_test-W200.graph" />
      <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
      <output name="island_filtered_output_file" file="test-W200-G600-E0.01-islandfiltered.bed" />
      <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-E0.01-islandfiltered-normalized.wig" />
      <output name="score_island_output_file" file="test_1_test-W200-G600-E0.01.scoreisland" />
      <output name="output_log_file" file="test_1_output_log_file.contains" compare="contains"/>
    </test>
    <test>
      <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
      <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" />
      <param name="fix_off_by_one_errors" />

      <param name="window_size" value="200" />
      <param name="fragment_size" value="150" />
      <param name="effective_genome_fraction" value="0.74" />
      <param name="gap_size" value="600" />
      <param name="error_cut_off" value="0.01" />
      <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
      <output name="redundancy_removed_control_bed_output_file" file="control-1-removed.bed" />
      <output name="summary_graph_output_file" file="test_1_test-W200.graph" />
      <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
      <output name="significant_islands_output_file" file="test_2_test-W200-G600-FDR0.01-island.bed" />
      <output name="island_filtered_output_file" file="test-W200-G600-FDR0.01-islandfiltered.bed" />
      <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />
      <output name="score_island_output_file" file="test_2_test-W200-G600.scoreisland" />
      <output name="islands_summary_output_file" file="test_2_test-W200-G600-islands-summary" />
      <output name="significant_islands_summary_output_file" file="test_2_test-W200-G600-islands-summary-FDR0.01" />
      <output name="output_log_file" file="test_2_output_log_file.contains" compare="contains"/>
    </test>
    <test>
      <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
      <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" />
      <param name="fix_off_by_one_errors" value="True" />

      <param name="window_size" value="200" />
      <param name="fragment_size" value="150" />
      <param name="effective_genome_fraction" value="0.74" />
      <param name="gap_size" value="600" />
      <param name="error_cut_off" value="0.01" />
      <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
      <output name="redundancy_removed_control_bed_output_file" file="control-1-removed.bed" />
      <output name="summary_graph_output_file" file="test_3_test-W200.graph" />
      <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
      <output name="significant_islands_output_file" file="test_3_test-W200-G600-FDR0.01-island.bed" />
      <output name="island_filtered_output_file" file="test-W200-G600-FDR0.01-islandfiltered.bed" />
      <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />
      <output name="score_island_output_file" file="test_3_test-W200-G600.scoreisland" />
      <output name="islands_summary_output_file" file="test_3_test-W200-G600-islands-summary" />
      <output name="significant_islands_summary_output_file" file="test_3_test-W200-G600-islands-summary-FDR0.01" />
      <output name="output_log_file" file="test_2_output_log_file.contains" compare="contains"/>
    </test>
    <test>
      <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
      <param name="input_control_file" />
      <param name="fix_off_by_one_errors" value="True" />

      <param name="window_size" value="200" />
      <param name="fragment_size" value="150" />
      <param name="effective_genome_fraction" value="0.74" />
      <param name="gap_size" value="600" />
      <param name="error_cut_off" value="0.01" />
      <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
      <output name="summary_graph_output_file" file="test_3_test-W200.graph" />
      <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
      <output name="island_filtered_output_file" file="test-W200-G600-E0.01-islandfiltered.bed" />
      <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-E0.01-islandfiltered-normalized.wig" />
      <output name="score_island_output_file" file="test_4_test-W200-G600-E0.01.scoreisland" />
      <output name="output_log_file" file="test_1_output_log_file.contains" compare="contains"/>
    </test>
  </tests>
  <help>
**What it does**