diff fastg2protlib-validate.xml @ 0:6b226c5907a1 draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastg2protlib-validate.xml	Fri Aug 07 06:17:31 2020 -0400
@@ -0,0 +1,41 @@
+<tool id="fastg2protlib-validate" name="FASTG2Protlib-Validate" version="@VERSION@">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="pkg_requirement" />
+    <description>Validate a candidate protein library</description>
+
+    <command detect_errors="exit_code">
+        <![CDATA[
+        python '$__tool_directory__/app_validate.py' 
+        -d '$database_file'
+        -f $fdr_level
+        -x '$decoy_header'
+        '$tabular_file'
+        ]]>
+    </command>
+    <inputs>
+        <param name="tabular_file" type="data" format="txt" label="MSGF+ tabular file" />
+        <param name="database_file" type="data" format="sqlite" label="Database Name"/>
+        <param name="fdr_level" type="float" value="0.10" label="FDR value for validation."/>
+        <param name="decoy_header" type="text" value="XXX_" label="Decoy protein header"/>
+    </inputs>
+    <outputs>
+        <data name="protein_fasta" format="fasta" from_work_dir="protein.fasta" label="Validated protein library"/>
+        <data name="protein_score" format="csv" from_work_dir="protein_scores.csv" label="Protein scores"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="tabular_file" value="mgf_tst.tab" />
+            <param name="database_file" value="tst_valid.db" />
+            <param name="fdr_level" value="0.10" />
+            <param name="decoy_header" value="XXX_" />
+            <output name="protein_fasta">
+                <assert_contents>
+                    <has_text text="RYSRPLSHL" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>    
+    <expand macro="help-text" />
+</tool>