--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hyphy_summary.xml	Wed Jun 09 07:03:54 2021 +0000
@@ -0,0 +1,198 @@
+<?xml version="1.0"?>
+<tool id="hyphy_summary" version="1.0.0" name="HyPhy-Summary" profile="21.01">
+    <description>generate summary report of HyPhy analyses</description>
+    <requirements>
+        <requirement type="package" version="0.19.7">python-bioext</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/scripts/hyphy_summary.py' 
+            --mode $mode_conditional.mode
+            #if $mode_conditional.mode == 'summary':
+                --combined '$mode_conditional.combined'
+                --pvalue $mode_conditional.pvalue
+                --gene '$mode_conditional.gene'
+                --labels '$mode_conditional.labels'
+                --default-tag '$mode_conditional.default_tag'
+                --name '$mode_conditional.name'
+                #if $mode_conditional.relax:
+                    --relax '$mode_conditional.relax'
+                #end if
+                #if $mode_conditional.busted:
+                    --busted '$mode_conditional.busted'
+                #end if
+                #if $mode_conditional.slac:
+                    --slac '$mode_conditional.slac'
+                #end if
+                #if $mode_conditional.fel:
+                    --fel '$mode_conditional.fel'
+                #end if
+                #if $mode_conditional.cfel:
+                    --cfel '$mode_conditional.cfel'
+                #end if
+                #if $mode_conditional.meme:
+                    --meme '$mode_conditional.meme'
+                #end if
+                #if $mode_conditional.meme_full:
+                    --meme-full '$mode_conditional.meme_full'
+                #end if
+                #if $mode_conditional.prime:
+                    --prime '$mode_conditional.prime'
+                #end if
+                #if $mode_conditional.fade:
+                    --fade '$mode_conditional.fade'
+                #end if
+                #if $mode_conditional.bgm:
+                    --bgm '$mode_conditional.bgm'
+                #end if
+            #else:
+                --annotation-inputs '$mode_conditional.annotation_inputs'
+                --summary-inputs '$mode_conditional.summary_inputs'
+            #end if
+            --annotation-output '$annotation'
+            --summary-output '$summary'
+    ]]></command>
+    <inputs>
+        <conditional name="mode_conditional">
+            <param argument="--mode" type="select" label="Mode">
+                <option value="summary">Generate gene summary</option>
+                <option value="merge">Merge gene summaries for clade analysis</option>
+            </param>
+            <when value="summary">
+                <param argument="--combined" type="data" format="fasta" label="Combined reference and query alignments from TN93-Filter" />
+                <param argument="--pvalue" type="float" min="0" max="1" value="0.05" label="p-value to use" />
+                <param argument="--labels" type="data" format="json,hyphy_results.json" label="HyPhy-Annotate branche labels in JSON format" />
+                <param argument="--gene" type="text" label="Name of the gene or sequence being analyzed">
+                    <sanitizer invalid_char="">
+                        <valid initial="string.ascii_letters,string.digits">
+                            <add value="_" />
+                            <add value="-" />
+                        </valid>
+                    </sanitizer>
+                </param>
+                <param argument="--default-tag" type="text" value="Reference" label="Default name for sequences that have no explicit label">
+                    <sanitizer invalid_char="">
+                        <valid initial="string.ascii_letters,string.digits">
+                            <add value="_" />
+                            <add value="-" />
+                        </valid>
+                    </sanitizer>
+                </param>
+                <param argument="--name" type="text" label="The sequence ID to highlight">
+                    <sanitizer invalid_char="">
+                        <valid initial="string.ascii_letters,string.digits">
+                            <add value="_" />
+                            <add value="-" />
+                        </valid>
+                    </sanitizer>
+                </param>
+                <param argument="--fade" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-FADE output dataset" />
+                <param argument="--prime" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-PRIME output dataset" />
+                <param argument="--relax" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-RELAX output dataset" />
+                <param argument="--meme" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-MEME output dataset" />
+                <param argument="--meme-full" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-MEME-Full output dataset" />
+                <param argument="--busted" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-BUSTED output dataset" />
+                <param argument="--slac" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-SLAC output dataset" />
+                <param argument="--fel" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-FEL output dataset" />
+                <param argument="--cfel" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-CFEL output dataset" />
+                <param argument="--bgm" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-BGM output dataset" />
+            </when>
+            <when value="merge">
+                <param argument="--summary-inputs" type="data" format="hyphy_results.json" multiple="true" label="Segment annotations to merge" />
+                <param argument="--annotation-inputs" type="data" format="hyphy_results.json" multiple="true" label="Site annotations to merge" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="summary" format="hyphy_results.json" label="${tool.name} on ${on_string} - Segment annotations" />
+        <data name="annotation" format="hyphy_results.json" label="${tool.name} on ${on_string} - Site annotations" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="mode" value="summary" />
+            <param name="name" value="epi_isl_1009769" />
+            <param name="gene" value="nsp8" />
+            <param name="combined" value="summary/nsp8.combined.fas" />
+            <param name="fade" value="summary/nsp8.FADE.json" />
+            <param name="prime" value="summary/nsp8.PRIME.json" />
+            <param name="relax" value="summary/nsp8.RELAX.json" />
+            <param name="meme" value="summary/nsp8.MEME.json" />
+            <param name="meme_full" value="summary/nsp8.MEME-full.json" />
+            <param name="labels" value="summary/nsp8.labels.json" />
+            <param name="busted" value="summary/nsp8.BUSTED.json" />
+            <param name="slac" value="summary/nsp8.SLAC.json" />
+            <param name="fel" value="summary/nsp8.FEL.json" />
+            <param name="cfel" value="summary/nsp8.CFEL.json" />
+            <param name="bgm" value="summary/nsp8.combined.fas.BGM.json" />
+            <output name="summary" file="summary/nsp8-segment.json" />
+            <output name="annotation" file="summary/nsp8-site.json" />
+        </test>
+        <test>
+            <param name="mode" value="summary" />
+            <param name="name" value="epi_isl_1009769" />
+            <param name="gene" value="ORF6" />
+            <param name="combined" value="summary/ORF6.combined.fas" />
+            <param name="fade" value="summary/ORF6.FADE.json" />
+            <param name="meme_full" value="summary/ORF6.MEME-full.json" />
+            <param name="labels" value="summary/ORF6.labels.json" />
+            <param name="slac" value="summary/ORF6.SLAC.json" />
+            <output name="summary" file="summary/ORF6-segment.json" />
+            <output name="annotation" file="summary/ORF6-site.json" />
+        </test>
+        <test>
+            <param name="mode" value="summary" />
+            <param name="name" value="epi_isl_1009769" />
+            <param name="gene" value="nsp7" />
+            <param name="combined" value="summary/nsp7.combined.fas" />
+            <param name="fade" value="summary/nsp7.FADE.json" />
+            <param name="meme_full" value="summary/nsp7.MEME-full.json" />
+            <param name="labels" value="summary/nsp7.labels.json" />
+            <param name="slac" value="summary/nsp7.SLAC.json" />
+            <output name="summary" file="summary/nsp7-segment.json" />
+            <output name="annotation" file="summary/nsp7-site.json" />
+        </test>
+        <test>
+            <param name="mode" value="merge" />
+            <param name="summary_inputs" value="summary/nsp7-segment.json,summary/nsp8-segment.json,summary/ORF6-segment.json" />
+            <param name="annotation_inputs" value="summary/nsp7-site.json,summary/nsp8-site.json,summary/ORF6-site.json" />
+            <output name="summary" file="summary/merged-segment.json" />
+            <output name="annotation" file="summary/merged-site.json" />
+        </test>
+    </tests>
+    <help><![CDATA[
+HyPhy-Summary
+=============
+
+This tool has two operation modes, summary and merge.
+
+Summary
+-------
+
+Given a combined and filtered alignment from TN93-Filter, along with the
+appropriate HyPhy analysis outputs, this mode will return two JSON files, one 
+with segment annotations and the other with site annotations.
+
+Analyses required for this mode:
+
+- FADE
+- PRIME
+- RELAX
+- MEME
+- MEME-Full
+- Annotate, with the labels in JSON format
+- BUSTED
+- SLAC
+- FEL
+- CFEL
+- BGM
+
+Merge
+-----
+
+This mode takes a set of segment and site annotations, one each per gene that
+was analyzed, and returns a merged set of site and segment annotations.
+
+]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/bti079</citation>
+    </citations>
+</tool>