diff sicer_wrapper.xml @ 3:5c2cc3b58c7d draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"

--- a/sicer_wrapper.xml	Wed Oct 24 11:31:03 2018 -0400
+++ b/sicer_wrapper.xml	Wed Oct 28 23:36:25 2020 +0000
@@ -1,155 +1,159 @@
-<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}'
-      --significant_islands_output_file "${significant_islands_output_file}"
-      --islands_summary_output_file "${islands_summary_output_file}"
-      --significant_islands_summary_output_file "${significant_islands_summary_output_file}"
-  #end if
-  ${fix_off_by_one_errors}
-  --dbkey '${input_bed_file.dbkey}'
-  --redundancy_threshold '${redundancy_threshold}'
-  --window_size '${window_size}'
-  --fragment_size '${fragment_size}'
-  --effective_genome_fraction '${effective_genome_fraction}'
-  --gap_size '${gap_size}'
-  --error_cut_off '${error_cut_off}'
-  ##output files
-  --stdout "${output_log_file}"
-  --redundancy_removed_test_bed_output_file "${redundancy_removed_test_bed_output_file}"
-  --redundancy_removed_control_bed_output_file "${redundancy_removed_control_bed_output_file}"
-  --score_island_output_file "${score_island_output_file}"
-  --summary_graph_output_file "${summary_graph_output_file}"
-  --test_normalized_wig_output_file "${test_normalized_wig_output_file}"
-  --island_filtered_output_file "${island_filtered_output_file}"
-  --island_filtered_normalized_wig_output_file "${island_filtered_normalized_wig_output_file}"
-  </command>
-  <requirements>
-    <requirement type="package" version="1.1">SICER</requirement>
-  </requirements>
-  <inputs>
-    <param name="input_bed_file" type="data" format="bed" label="ChIP-Seq Tag File" >
-      <validator type="expression" message="SICER is not available for the genome.">value is not None and value.dbkey in [ 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ]</validator>
-    </param>
-    <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" optional="True"> <!-- fix me, add filter to match dbkeys -->
-      <options>
-        <filter type="data_meta" ref="input_bed_file" key="dbkey" />
-      </options>
-    </param>
-    <param name="fix_off_by_one_errors" type="boolean" truevalue="--fix_off_by_one_errors" falsevalue="" checked="True" label="Fix off-by-one errors in output files" help="SICER creates non-standard output files, this option will fix these coordinates"/> 
-    <param name="redundancy_threshold" type="integer" label="Redundancy Threshold" value="1" help="The number of copies of identical reads allowed in a library" />
-    <param name="window_size" type="integer" label="Window size" value="200" help="Resolution of SICER algorithm. For histone modifications, one can use 200 bp" />
-    <param name="fragment_size" type="integer" label="Fragment size" value="150" help="for determination of the amount of shift from the beginning of a read to the center of the DNA fragment represented by the read. FRAGMENT_SIZE=150 means the shift is 75." />
-    <param name="effective_genome_fraction" type="float" label="Effective genome fraction" value="0.74" help="Effective Genome as fraction of the genome size. It depends on read length." />
-    <param name="gap_size" type="integer" label="Gap size" value="600" help="Needs to be multiples of window size. Namely if the window size is 200, the gap size should be 0, 200, 400, 600, ..." />
-    <param name="error_cut_off" type="float" label="Statistic threshold value" value="0.01" help="FDR (with control) or E-value (without control)" />
-  </inputs>
-  <outputs>
-    <data name="redundancy_removed_test_bed_output_file" format="bed" label="${tool.name} on ${on_string} (test-${redundancy_threshold}-removed.bed)"/>
-    <data name="redundancy_removed_control_bed_output_file" format="bed" label="${tool.name} on ${on_string} (control-${redundancy_threshold}-removed.bed)">
-      <filter>input_control_file is not None</filter>
-    </data>
-    <data name="summary_graph_output_file" format="bedgraph" label="${tool.name} on ${on_string} (test-W${window_size}.graph)"/>
-    <data name="test_normalized_wig_output_file" format="wig" label="${tool.name} on ${on_string} (test-W${window_size}-normalized.wig)"/>
-    <data name="significant_islands_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-FDR${error_cut_off}-island.bed)">
-      <filter>input_control_file is not None</filter>
-    </data>
-    <data name="island_filtered_output_file" format="bed" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '-FDR', $error_cut_off, '-islandfiltered.bed' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '-islandfiltered.bed' ] ) ) #)"/>
-    <data name="island_filtered_normalized_wig_output_file" format="wig" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '-FDR', $error_cut_off, '-islandfiltered-normalized.wig' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '-islandfiltered-normalized.wig' ] ) ) #)"/>
-    <data name="score_island_output_file" format="interval" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '.scoreisland' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '.scoreisland' ] ) ) #)"/>
-    <data name="islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary)">
-      <filter>input_control_file is not None</filter>
-    </data>
-    <data name="significant_islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary-FDR${error_cut_off})">
-      <filter>input_control_file is not None</filter>
-    </data>
-    <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/>
-  </outputs>
-  <tests>
-    <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" />
-      <param name="redundancy_threshold" value="1" />
-      <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="redundancy_threshold" value="1" />
-      <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="redundancy_threshold" value="1" />
-      <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="redundancy_threshold" value="1" />
-      <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>
+<tool id="peakcalling_sicer" name="SICER" version="@TOOL_VERSION@">
+    <description>Statistical approach for the Identification of ChIP-Enriched Regions</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.1</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">SICER</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/sicer_wrapper.py'
+--bed_file '${input_bed_file}' 
+#if str($input_control_file) != 'None':
+    --control_file '${input_control_file}'
+    --significant_islands_output_file "${significant_islands_output_file}"
+    --islands_summary_output_file "${islands_summary_output_file}"
+    --significant_islands_summary_output_file "${significant_islands_summary_output_file}"
+#end if
+${fix_off_by_one_errors}
+--dbkey '${input_bed_file.dbkey}'
+--redundancy_threshold '${redundancy_threshold}'
+--window_size '${window_size}'
+--fragment_size '${fragment_size}'
+--effective_genome_fraction '${effective_genome_fraction}'
+--gap_size '${gap_size}'
+--error_cut_off '${error_cut_off}'
+##output files
+--stdout "${output_log_file}"
+--redundancy_removed_test_bed_output_file "${redundancy_removed_test_bed_output_file}"
+--redundancy_removed_control_bed_output_file "${redundancy_removed_control_bed_output_file}"
+--score_island_output_file "${score_island_output_file}"
+--summary_graph_output_file "${summary_graph_output_file}"
+--test_normalized_wig_output_file "${test_normalized_wig_output_file}"
+--island_filtered_output_file "${island_filtered_output_file}"
+--island_filtered_normalized_wig_output_file "${island_filtered_normalized_wig_output_file}"
+    ]]></command>
+    <inputs>
+        <param name="input_bed_file" type="data" format="bed" label="ChIP-Seq Tag File" >
+            <validator type="expression" message="SICER is not available for the genome.">value is not None and value.dbkey in ['mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8']</validator>
+        </param>
+        <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" optional="true"> <!-- fix me, add filter to match dbkeys -->
+            <options>
+                <filter type="data_meta" ref="input_bed_file" key="dbkey" />
+            </options>
+        </param>
+        <param name="fix_off_by_one_errors" type="boolean" truevalue="--fix_off_by_one_errors" falsevalue="" checked="true" label="Fix off-by-one errors in output files" help="SICER creates non-standard output files, this option will fix these coordinates"/> 
+        <param name="redundancy_threshold" type="integer" label="Redundancy Threshold" value="1" help="The number of copies of identical reads allowed in a library" />
+        <param name="window_size" type="integer" value="200" label="Window size" help="Resolution of SICER algorithm. For histone modifications, one can use 200 bp" />
+        <param name="fragment_size" type="integer" value="150" label="Fragment size" help="for determination of the amount of shift from the beginning of a read to the center of the DNA fragment represented by the read. FRAGMENT_SIZE=150 means the shift is 75." />
+        <param name="effective_genome_fraction" type="float" value="0.74" label="Effective genome fraction" help="Effective Genome as fraction of the genome size. It depends on read length." />
+        <param name="gap_size" type="integer" value="600" label="Gap size" help="Needs to be multiples of window size. Namely if the window size is 200, the gap size should be 0, 200, 400, 600, ..." />
+        <param name="error_cut_off" type="float" value="0.01" label="Statistic threshold value" help="FDR (with control) or E-value (without control)" />
+    </inputs>
+    <outputs>
+        <data name="redundancy_removed_test_bed_output_file" format="bed" label="${tool.name} on ${on_string} (test-${redundancy_threshold}-removed.bed)"/>
+        <data name="redundancy_removed_control_bed_output_file" format="bed" label="${tool.name} on ${on_string} (control-${redundancy_threshold}-removed.bed)">
+            <filter>input_control_file is not None</filter>
+        </data>
+        <data name="summary_graph_output_file" format="bedgraph" label="${tool.name} on ${on_string} (test-W${window_size}.graph)"/>
+        <data name="test_normalized_wig_output_file" format="wig" label="${tool.name} on ${on_string} (test-W${window_size}-normalized.wig)"/>
+        <data name="significant_islands_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-FDR${error_cut_off}-island.bed)">
+            <filter>input_control_file is not None</filter>
+        </data>
+        <data name="island_filtered_output_file" format="bed" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '-FDR', $error_cut_off, '-islandfiltered.bed' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '-islandfiltered.bed' ] ) ) #)"/>
+        <data name="island_filtered_normalized_wig_output_file" format="wig" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '-FDR', $error_cut_off, '-islandfiltered-normalized.wig' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '-islandfiltered-normalized.wig' ] ) ) #)"/>
+        <data name="score_island_output_file" format="interval" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '.scoreisland' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '.scoreisland' ] ) ) #)"/>
+        <data name="islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary)">
+            <filter>input_control_file is not None</filter>
+        </data>
+        <data name="significant_islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary-FDR${error_cut_off})">
+            <filter>input_control_file is not None</filter>
+        </data>
+        <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/>
+    </outputs>
+    <tests>
+        <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" />
+            <param name="redundancy_threshold" value="1" />
+            <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="redundancy_threshold" value="1" />
+            <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="redundancy_threshold" value="1" />
+            <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="redundancy_threshold" value="1" />
+            <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><![CDATA[
 **What it does**
 
 SICER first and foremost is a filtering tool. Its main functions are::
@@ -170,9 +174,8 @@
 
 **Citation**
 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
-
-  </help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btp340</citation>
-  </citations>
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btp340</citation>
+    </citations>
 </tool>