--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BlastParser_and_hits.xml	Sun Oct 15 18:43:37 2017 -0400
@@ -0,0 +1,94 @@
+<tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.5.0">
+<description>for virus discovery</description>
+<requirements></requirements>
+<command><![CDATA[
+    python '$__tool_directory__'/BlastParser_and_hits.py
+	--sequences '$sequences'
+	--blast '$blast'
+	--tabularOutput '$tabularOutput'
+	--fastaOutput '$fastaOutput'
+	--flanking $flanking
+	--mode $mode
+	## Additional parameters.
+    #if $additional_filters.use_filters == "yes":
+        --filter_relativeCov $additional_filters.filter_relativeCov
+        --filter_maxScore $additional_filters.filter_maxScore
+        --filter_meanScore $additional_filters.filter_meanScore
+        --filter_term_in "$additional_filters.filter_term_in"
+        --filter_term_out "$additional_filters.filter_term_out"
+    #end if
+    --al_sequences '$al_sequences'
+    --un_sequences '$un_sequences'
+    --dataset_name "$blast.element_identifier"
+
+    ]]></command>
+<inputs>
+	<param name="sequences" type="data" format="fasta"  label="fasta sequences that have been blasted" />
+	<param name="blast" type="data" format="tabular" label="The blast output you wish to parse">
+            <validator type="expression" message="Blast file must have 13 columns">value.metadata.columns == 13</validator>
+        </param>
+	<param name="flanking" type="integer" value= "5" label="Number of flanking nucleotides to add to hits for CAP3 assembly"/>
+	<param name="mode" type="select" label="Extensive or compact  reporting mode" help="display (extensive)  or not (compact) the oases contigs">
+	    <option value="verbose" selected="true">extensive</option>
+	    <option value="short">compact</option>
+	</param>
+    <conditional name="additional_filters">
+            <param name="use_filters" type="select" label="Use Additional Filters?">
+                <option value="no">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no">
+            </when>
+            <when value="yes">            
+                <param name="filter_relativeCov" type="float" value="0" max="1" label="Minimum Relative Subject Coverage" help=""/>
+                <param name="filter_maxScore" type="float" value="0" label="Minimum maximum BitScore" help=""/>
+                <param name="filter_meanScore" type="float" value="0" label="Minimum mean BitScore" help=""/>
+                <param name="filter_term_in" type="text" value="" label="filter the subject list with a keyword" help=""/>
+                <param name="filter_term_out" type="text" value="" label="filter the subject list excluding a keyword" help=""/>
+            </when>
+    </conditional>
+</inputs>
+<outputs>
+	<data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/>
+	<data name="fastaOutput" format="fasta" label="hits"/>
+	<data name="al_sequences" format="fasta" label="Blast aligned sequences"/>
+	<data name="un_sequences" format="fasta" label="Blast unaligned sequences"/>
+</outputs>
+
+  <tests>
+    <test>
+        <param ftype="fasta" name="sequences" value="input.fa" />
+        <param ftype="tabular" name="blast" value="blast.tab" />
+        <param name="flanking" value="5" />
+        <param name="use_filters" value="no" />
+        <param name="mode" value="verbose" />
+        <output name="tabularOutput" ftype="tabular" file="output.tab" />
+        <output name="fastaOutput" ftype="fasta" file="output.fa" />
+        <output name="al_sequences" ftype="fasta" file="al_sequences.fa" />
+        <output name="un_sequences" ftype="fasta" file="un_sequences.fa" />
+    </test>
+  </tests>
+
+<help>
+
+**What it does**
+
+Parse blast output for viruses genome assembly.
+
+Takes as inputs
+
+ - 1. the fasta sequences that have been submitted to blast
+ - 2. a blast alignment in a tabular format. **Importantly** this tabular output must contains the 12 standard columns (see blast documentation), **plus a column 13** that will report the length of the subject sequence (slen). When you use blast tools prior using this tool, remember to **check the appropriate box** to get the 13th column in the blast tabular output.
+ - 3. the numbers of flanking nucleotides to be recovered at the ends of blast hit sequences
+
+The tool returns 4 datasets
+
+ - 1. the fasta input sequences that produced significant blast hits
+ - 2. the fasta sequences that did not produced significant blast hits
+ - 3. the sequences of the blast hits, plus the flanking sequences (as specified in the tool form). This dataset may be further used in metavisitor workflows to produce contigs of hits.
+ - 4. and the parsing of the blast alignments which summarizes the blast results by "subject" sequences (blast analysis, by subjects)
+
+This latter parsing dataset may be customized by tuning the reporting mode and/or using filters
+
+</help>
+</tool>