changeset 0:8d9746627f77 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig commit 8d5424b11bc4d5a4112b030dc38016e4d8b60e21

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deepsig.xml	Tue May 23 17:04:29 2023 +0000
@@ -0,0 +1,76 @@
+<?xml version="1.0"?>
+<tool id="deepsig" name="DeepSig" version="@TOOL_VERSION@+galaxy0" profile="21.05">
+    <description>signal peptides predictor</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">deepsig</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        deepsig
+        -f '$input_fasta'
+        -o '$output'
+        -k $organism
+        -m $output_format
+        -t \${GALAXY_SLOTS:-1}
+        
+    ]]></command>
+
+    <inputs>
+        <param name="input_fasta" argument="-f" type="data" format="fasta" label="Protein sequences"/>
+        <param name="organism" argument="-k" type="select" label="Taxonomic domain">
+            <option value="euk" selected="true">Eukaryotes</option>
+            <option value="gramp">Gram-positive</option>
+            <option value="gramn">Gram-negative</option>
+        </param>
+
+        <param name="output_format" argument="-m" type="select" label="output_format">
+            <option value="gff3" selected="true">GFF3</option>
+            <option value="json">JSON</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="gff3" label="DeepSig on ${on_string}">
+            <change_format>
+                <when input="output_format" value="json" format="json"/>
+            </change_format>
+        </data>
+    </outputs>
+
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_fasta" value="G5ED35.fasta"/>
+            <param name="organism" value="euk"/>
+            <param name="output_format" value="gff3"/>
+            <output name="output" ftype="gff3">
+                <assert_contents>
+                    <has_text text="sp|G5ED35|TTR52_CAEEL"/>
+                    <has_text text="evidence=ECO:0000256"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_fasta" value="G5ED35.fasta"/>
+            <param name="organism" value="euk"/>
+            <param name="output_format" value="json"/>
+            <output name="output" ftype="json">
+                <assert_contents>
+                    <has_text text='"sequence": "MSRFLIYFLPFFIYSGNVLSKTSCLMATGVLKCPTDPEAVKKVHIDLWDEDSLPLESDDLMGRTWSDRNGNFQVTGCASDFGPINTPDPYLYIQHNCPHRDSNATNPIQIDVIPLFLPSIVRLGNVYLDRYLEDY"'/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+        deepsig_  Predictor of signal peptides in proteins based on deep learning.
+        DeepSig is a novel approach to predict signal peptides in proteins based on 
+        deep learning and sequence labelling methods. The proposed approach was 
+        evaluated and compared with other available predictors, including the top-performing SignalP.
+
+        .. _deepsig: https://github.com/BolognaBiocomp/deepsig
+    ]]></help>
+
+<expand macro="citation"></expand>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue May 23 17:04:29 2023 +0000
@@ -0,0 +1,8 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.2.5</token>
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/btx818</citation> 
+        </citations>
+    </xml>
+</macros>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/G5ED35.fasta	Tue May 23 17:04:29 2023 +0000
@@ -0,0 +1,4 @@
+>sp|G5ED35|TTR52_CAEEL Transthyretin-like protein 52 OS=Caenorhabditis elegans OX=6239 GN=ttr-52 PE=1 SV=1
+MSRFLIYFLPFFIYSGNVLSKTSCLMATGVLKCPTDPEAVKKVHIDLWDEDSLPLESDDL
+MGRTWSDRNGNFQVTGCASDFGPINTPDPYLYIQHNCPHRDSNATNPIQIDVIPLFLPSI
+VRLGNVYLDRYLEDY