diff netmhciipan.xml @ 0:4fb283cf23a5 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/netmhciipan.xml	Wed Jul 09 12:56:02 2025 +0000
@@ -0,0 +1,104 @@
+<tool id="iedb_netmhciipan" name="NetMHCiiPan" version="4.1+galaxy0" profile="24.2">
+    <description>MHCii Binding prediction</description>
+    <macros>
+        <import>netmhciipan_alleles_macros.xml</import>
+        <import>shared_macros.xml</import>
+    </macros>
+    <requirements>
+        <expand macro="requirements" />
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+        #import re
+
+        python '${__tool_directory__}/nextgen_iedb_api.py'
+        --tool-group=mhcii
+        #for $method in $methods:
+          --method=$method
+        #end for
+
+        #if $alleles.allelesrc == 'history':
+          -A '$alleles.allele_file'
+        #else:
+          -A '$entered_alleles'
+        #end if
+        #if $inversion == 'true'
+          -R
+        #end if
+        -l '$length_start','$length_end'
+        -P '$peptide_shift'
+
+        #if $sequence.seqsrc == 'fasta':
+          -i '$sequence.seq_fasta'
+        #else if $sequence.seqsrc == 'tabular':
+          -i '$sequence.seq_tsv'
+          -c #echo int(str($sequence.pep_col)) - 1
+        #else:
+          -i '$entered_seqs' -c 0
+        #end if
+
+        -o '$output'
+    ]]></command>
+    <configfiles>
+        <expand macro="configfiles" />
+    </configfiles>
+    <inputs>
+        <param name="methods" type="select" multiple="true" label="prediction method">
+            <option value="netmhciipan_el" selected="true">netmhciipan_el</option>
+            <option value="netmhciipan_ba">netmhciipan_ba</option>
+        </param>
+        <expand macro="inputs" hla_examples="DPA1*01/DPB1*04:01 HLA-DRB1*01:01 H2-IAb"/>
+        <param name="peptide_shift" type="integer" value="5" label="Peptide shift"/>
+        <param name="inversion" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add reversed peptides to input database"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" label="IEDB NetMHCiiPan ${methods}"/>
+    </outputs>
+    <tests>
+        <!-- test1 -->
+        <test expect_num_outputs="1">
+            <param name="alleles|allelesrc" value="entry"/>
+            <param name="alleles|allele_text" value="HLA-DQA1*03:01/DQB1*06:02 HLA-DQA1*03:01/DQB1*06:04"/>
+            <param name="methods" value="netmhciipan_ba,netmhciipan_el"/>
+            <param name="length_start" value="13"/>
+            <param name="length_end" value="17"/>
+            <param name="sequence|seqsrc" value="entry"/>
+            <param name="sequence|seq_text" value="SLYNTVATLYCVHQRIDV"/>
+            <param name="inversion" value="true"/>
+            <output name="output" file="outputs/netmhciipan_output_1.tsv"/>
+        </test>
+        <!-- test2 -->
+        <test expect_num_outputs="1">
+            <param name="alleles|allelesrc" value="history"/>
+            <param name="alleles|allele_file" value="netmhciipan_alleles.txt"/>
+            <param name="length_start" value="13"/>
+            <param name="length_end" value="17"/>
+            <param name="sequence|seqsrc" value="tabular"/>
+            <param name="sequence|seq_tsv" value="seqs.tsv"/>
+            <param name="sequence|pep_col" value="3"/>
+            <param name="inversion" value="true"/>
+            <output name="output" file="outputs/netmhciipan_output_2.tsv"/>
+        </test>
+        <!-- test3 -->
+        <test expect_num_outputs="1">
+            <param name="alleles|allelesrc" value="history"/>
+            <param name="alleles|allele_file" value="netmhciipan_alleles.txt"/>
+            <param name="length_start" value="13"/>
+            <param name="length_end" value="17"/>
+            <param name="peptide_shift" value="6"/>
+            <param name="sequence|seqsrc" value="fasta"/>
+            <param name="sequence|seq_fasta" value="seqs.fa"/>
+            <param name="inversion" value="true"/>
+            <output name="output" file="outputs/netmhciipan_output_3.tsv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+The NetMHCiipan-4.1 server predicts binding of peptides to any MHC II molecule of known sequence using artificial neural networks (ANNs).
+
+This tool uses the "Next-Generation IEDB Tools" API to submit NetMHCiipan-4.1 jobs and retrieve results.
+IEDB is a free resource, funded by a contract from the National Institute of Allergy and Infectious Diseases.
+    ]]></help>
+    <citations>
+        <expand macro="citations" />
+    </citations>
+</tool>