diff encyclopedia_fasta_to_prosit_csv.xml @ 0:88d3243c483f draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/encyclopedia_fasta_to_prosit_csv.xml	Mon Sep 14 16:57:58 2020 +0000
@@ -0,0 +1,62 @@
+<tool id="encyclopedia_fasta_to_prosit_csv" name="ConvertFastaToPrositCSV" version="@VERSION@.0" python_template_version="3.5">
+    <description>Create Prosit CSV Input From a Protein FASTA</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="aggressive"><![CDATA[
+        EncyclopeDIA -convert -fastatoprositcsv
+        -i '$i'
+        -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}"
+        -minCharge $minCharge
+        -maxCharge $maxCharge
+        -defaultCharge $defaultCharge
+        -maxMissedCleavage $maxMissedCleavage
+        -minMz $minMz
+        -maxMz $maxMz
+        -defaultNCE $defaultNCE
+        #if $enzyme
+            -enzyme '$enzyme'
+        #end if
+        -o '$output'
+    ]]></command>
+    <inputs>
+        <param argument="-i" type="data" format="fasta" label="Protein Fasta database"/>
+        <param argument="-minCharge" type="integer" value="2" min="1" max="6" label="minCharge"/>
+        <param argument="-maxCharge" type="integer" value="3" min="1" max="6" label="maxCharge"/>
+        <param argument="-defaultCharge" type="integer" value="3" min="1" max="4" label="defaultCharge"/>
+        <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="3" label="maxMissedCleavage"/>
+        <param argument="-minMz" type="float" value="396.4" min="150.0" max="1600.0" label="minMz"/>
+        <param argument="-maxMz" type="float" value="1002.7" min="150.0" max="1600.0" label="maxMz"/>
+        <param argument="-defaultNCE" type="integer" value="33" min="25" max="40" label="Normalized Collision Energy"/>
+        <param argument="-enzyme" type="select" optional="true" label="Digestion Enzyme">
+            <option value="Trypsin">Trypsin</option>
+            <option value="Lys-C">Lys-C</option>
+            <option value="Lys-N">Lys-N</option>
+            <option value="Arg-C">Arg-C</option>
+            <option value="Glu-C">Glu-C</option>
+            <option value="CNBr">CNBr</option>
+            <option value="Chymotrypsin">Chymotrypsin</option>
+            <option value="Pepsin A">Pepsin A</option>
+            <option value="No Enzyme">No Enzyme</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="csv" label="${i.name} Prosit_input.csv"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="i" ftype="fasta" value="YeastProteinFasta5.fasta"/>
+            <output name="output" ftype="csv">
+                <assert_contents>
+                    <has_text text="collision_energy"/>
+                    <has_text text="EDFFTVFDSLLR"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Create Prosit CSV From FASTA
+    ]]></help>
+    <expand macro="citations" />
+</tool>