diff exonerate.xml @ 0:f48ed38dfddf draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit e02d20338ee01ed58265d93e9cc5b0695a322d47

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/exonerate.xml	Thu Aug 02 09:11:30 2018 -0400
@@ -0,0 +1,168 @@
+<tool id="exonerate" name="Exonerate" profile="16.04" version="@VERSION@">
+    <description>pairwise sequence comparison</description>
+    <macros>
+	<import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command><![CDATA[
+        exonerate
+
+        --query '$query'
+
+        #if str( $ref_seq.ref_seq_selector ) == "personal"
+            --target '${ref_seq.input_fasta}'
+        #else
+            --target '${ref_seq.input_fasta.fields.path}'
+        #end if
+
+        --score $score
+        --percent $percent
+        --bestn $bestn
+        --verbose 0
+
+        #if str($model) != "ungapped"
+            --model '${model}'
+        #end if
+
+        #if str($model) == "est2genome"
+            --querytype dna --targettype dna
+        #elif str($model) == "protein2genome"
+            --querytype protein --targettype dna
+        #elif str($model) == "coding2coding"
+            --querytype dna --targettype dna
+        #end if
+
+        #if str($outformat) == "alignment"
+            --showalignment yes --showvulgar no > '${output_ali}'
+        #elif str($outformat) == "targetgff"
+            --showalignment no --showvulgar no --showtargetgff yes --showquerygff no > '${output_gff}'
+        #elif str($outformat) == "querygff"
+            --showalignment no --showvulgar no --showtargetgff no --showquerygff yes > '${output_gff}'
+        #end if
+    ]]></command>
+
+    <inputs>
+        <param argument="--query" type="data" format="fasta" label="Select the query sequence(s) in fasta" />
+
+        <conditional name="ref_seq">
+            <param name="ref_seq_selector" type="select" label="Reference sequence(s)">
+                <option selected="True" value="database">Use a built-in genome</option>
+                <option value="personal">Use a genome from history</option>
+            </param>
+            <when value="database">
+                <param
+                  help="If your genome of interest is not listed, contact the Galaxy server administrators"
+                  label="Reference sequence(s)"
+                  name="input_fasta"
+                  type="select"
+                  >
+                    <options from_data_table="all_fasta">
+                        <filter column="2" type="sort_by" />
+                        <validator message="No sequences are available" type="no_options" />
+                    </options>
+                </param>
+            </when>
+            <when value="personal">
+                <param name="input_fasta" type="data" format="fasta" label="Reference sequence(s)" />
+            </when>
+        </conditional>
+
+        <param name='model' type='select' label="Alignment method">
+            <option value="ungapped" selected="true">Simple ungapped alignment</option>
+            <option value="est2genome">est2genome: align cDNA to a genome</option>
+            <option value="protein2genome">protein2genome: align proteins to a genome</option>
+            <option value="coding2coding">coding2coding: 6-frame translated alignment of DNA sequences</option>
+        </param>
+        <param name='outformat' type='select' label="Output format">
+            <option value="targetgff" selected="true">GFF on target sequence(s)</option>
+            <option value="querygff">GFF on query sequence(s)</option>
+            <option value="alignment">Human readable alignment</option>
+        </param>
+        <param name='score' type='integer' min="0" max="10000" value="100" label="Score threshold for gapped alignment"/>
+        <param name='percent' type='float' min="0" max="100" value="0.0" label="Report alignment over a percentage of the maximum score attainable by each query"/>
+        <param name='bestn' type='integer' min="0" max="10000" value="0" label="Report best N results per query (0 to report all)"/>
+    </inputs>
+    <outputs>
+        <data name="output_gff" format="txt" label="${tool.name} on $on_string">
+            <filter>outformat != 'alignment'</filter>
+        </data>
+        <data name="output_ali" format="gff" label="${tool.name} on $on_string">
+            <filter>outformat == 'alignment'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="query" value="genome.fa"/>
+            <conditional name="ref_seq">
+                <param name="ref_seq_selector" value="personal"/>
+                <param name="input_fasta" value="genome.fa"/>
+            </conditional>
+            <param name="outformat" value="targetgff"/>
+            <output name="output_gff" file="out_target.gff"/>
+        </test>
+        <test>
+            <param name="query" value="genome.fa"/>
+            <conditional name="ref_seq">
+                <param name="ref_seq_selector" value="database"/>
+                <param name="input_fasta" value="merlin"/>
+            </conditional>
+            <param name="outformat" value="targetgff"/>
+            <output name="output_gff" file="out_target.gff"/>
+        </test>
+        <test>
+            <param name="query" value="genome.fa"/>
+            <conditional name="ref_seq">
+                <param name="ref_seq_selector" value="personal"/>
+                <param name="input_fasta" value="genome.fa"/>
+            </conditional>
+            <param name="outformat" value="querygff"/>
+            <output name="output_gff" file="out_query.gff"/>
+        </test>
+        <test>
+            <param name="query" value="genome.fa"/>
+            <conditional name="ref_seq">
+                <param name="ref_seq_selector" value="personal"/>
+                <param name="input_fasta" value="genome.fa"/>
+            </conditional>
+            <param name="outformat" value="alignment"/>
+            <output name="output_ali" file="out.txt"/>
+        </test>
+        <test>
+            <param name="query" value="transcriptome.fa"/>
+            <conditional name="ref_seq">
+                <param name="ref_seq_selector" value="personal"/>
+                <param name="input_fasta" value="genome.fa"/>
+            </conditional>
+            <param name="model" value="est2genome"/>
+            <param name="outformat" value="targetgff"/>
+            <output name="output_gff" file="est2genome.gff"/>
+        </test>
+        <test>
+            <param name="query" value="proteome.fa"/>
+            <conditional name="ref_seq">
+                <param name="ref_seq_selector" value="personal"/>
+                <param name="input_fasta" value="genome.fa"/>
+            </conditional>
+            <param name="model" value="protein2genome"/>
+            <param name="outformat" value="targetgff"/>
+            <output name="output_gff" file="protein2genome.gff"/>
+        </test>
+        <test>
+            <param name="query" value="genome.fa"/>
+            <conditional name="ref_seq">
+                <param name="ref_seq_selector" value="personal"/>
+                <param name="input_fasta" value="genome.fa"/>
+            </conditional>
+            <param name="model" value="coding2coding"/>
+            <param name="outformat" value="targetgff"/>
+            <output name="output_gff" file="coding2coding.gff"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Exonerate is a generic tool for pairwise sequence comparison.
+        It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.
+
+        .. _Exonerate website: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate
+    ]]></help>
+    <expand macro="citations"/>
+</tool>