diff fasta_cli.xml @ 0:8b99cb00e1c4 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta_cli.xml	Tue May 15 14:50:35 2018 -0400
@@ -0,0 +1,63 @@
+<tool id="fasta_cli" name="FastaCLI" version="1.0">
+    <description>
+        Appends decoy sequences to FASTA files
+    </description>
+    <macros>
+        <import>macros_basic.xml</import>
+    </macros>
+    <requirements>
+	<requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
+	<requirement type="package" version="3.0">zip</requirement>
+    </requirements>
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+
+        ## #set $temp_stderr = "searchgui_stderr"
+        #set $bin_dir = "bin"
+
+        mkdir output;
+        cwd=`pwd`;
+        export HOME=\$cwd;
+
+        ## echo the search engines to run
+        ##echo "$search_engines_options.engines";
+        echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}";
+
+        cp "${input_database}" input_database.fasta;
+
+        ###########################################
+        ####       Creating decoy database     ####
+        ###########################################
+
+        echo "Creating decoy database.";
+        searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\$cwd/${bin_dir}" -in input_database.fasta -decoy &&
+        rm input_database.fasta;
+        echo "Decoy database:";
+        echo "\$cwd/input_database_concatenated_target_decoy.fasta";
+
+        exit_code_for_galaxy=\$?;
+        ## cat $temp_stderr 2>&1;
+        (exit \$exit_code_for_galaxy)
+]]>
+    </command>
+    <inputs>
+        <param format="fasta" name="input_database" type="data" label="Protein Database"
+            help="Select FASTA database from history"/>
+    </inputs>
+    <outputs>
+        <data name="input_database_concatenated_target_decoy" format="fasta" from_work_dir="input_database_concatenated_target_decoy.fasta" label="${tool.name}: FASTA file with decoys on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
+            <output name="input_database_concatenated_target_decoy" file="searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" compare="sim_size" delta="1000" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Appends decoy sequences to FASTA files.
+    </help>
+    <expand macro="citations" />
+</tool>