diff pvac-seq.xml @ 0:916372196ae8 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pvac-seq.xml	Mon Jul 15 05:23:00 2019 -0400
@@ -0,0 +1,57 @@
+<tool id="pvac-seq" name="PVAC-seq" version="0.1.0">
+    <command detect_errors="exit_code"><![CDATA[
+        #if str( $epitope_length ) != "":
+            #set $epitope_length = "-e " + str($epitope_length)
+        #end if
+        #set algs = ' '.join([str($alg) for $alg in $algorithms]) 
+        pvacseq run 
+        ${epitope_length} 
+        --tdna-vaf ${tdna_vaf} 
+        --net-chop-method ${net_chop_method} 
+        ${net_mhc_stab}
+        --top-score-metric ${top_score_metric}
+        --downstream-sequence-length ${downstream_sequence_length}
+        ${input_vcf} 
+        galaxy 
+        ${allele} 
+        ${algs} 
+        `pwd` && mv MHC_Class_II/galaxy.final.tsv $output
+
+    ]]></command>
+    <inputs>
+        <param type="data" name="input_vcf" format="vcf" />
+        <param type="text" name="allele" />
+        <param name="algorithms" type="select" multiple="true" label="Epitope prediction algorithms">
+            <option value="NNalign">NNalign</option>
+            <option value="NetMHC">NetMHC</option>
+            <option value="NetMHCIIpan">NetMHCIIpan</option>
+            <option value="NetMHCcons">NetMHCcons</option>
+            <option value="NetMHCpan">NetMHCpan</option>
+            <option value="PickPocket">PickPocket</option>
+            <option value="SMMPMBEC">SMMPMBEC</option>
+            <option value="SMMalign">SMMalign</option>
+        </param>
+
+        <param type="text" name="epitope_length"/>
+        <param type="text" name="downstream_sequence_length" value="1000" help="int or 'full'"/>
+        <param type="text" name="tdna_vaf" value="40"/>
+        <param name="net_chop_method" type="select" label="NetChop prediction method">
+            <option value="cterm">cterm</option>
+            <option value="20s">20S</option>
+        </param>
+        <param name="net_mhc_stab" type="select" label="Run NetMHCStabPan after all filtering?">
+            <option value="--netmhc-stab">Yes</option>
+            <option value="">No</option>
+        </param>
+        <param name="top_score_metric" type="select" label="The ic50 scoring metric to use">
+            <option value="median">Median</option>
+            <option value="lowest">Lowest</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular"/>
+    </outputs>
+    <help><![CDATA[
+        TODO: Fill in help.
+    ]]></help>
+</tool>
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