Mercurial > repos > devteam > sicer

diff sicer_wrapper.xml @ 2:74c9214cc8e6 draft

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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 11:31:03 -0400
parents 4a14714649b4
children 5c2cc3b58c7d
line wrap: on
line diff
--- a/sicer_wrapper.xml	Tue Jul 21 15:59:56 2015 -0400
+++ b/sicer_wrapper.xml	Wed Oct 24 11:31:03 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="peakcalling_sicer" name="SICER" version="0.0.1">
+<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}' 
@@ -78,13 +78,13 @@
       <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"/>
+      <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" />
@@ -96,17 +96,17 @@
       <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"/>
+      <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" />
@@ -118,17 +118,17 @@
       <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"/>
+      <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" />
@@ -140,13 +140,13 @@
       <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"/>
+      <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>