Mercurial > repos > sanbi-uwc > build_ctb_gene

changeset 4:714cbeae0b96 draft

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
author sanbi-uwc
date Mon, 16 May 2016 04:20:19 -0400
parents 65558b5914fc
children 6098213127d7
files build_ctb_gene.py build_ctb_gene.xml
diffstat 2 files changed, 107 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build_ctb_gene.py	Mon May 16 04:20:19 2016 -0400
@@ -0,0 +1,61 @@
+#!/usr/bin/env python
+from __future__ import print_function
+import argparse
+import os
+import sys
+import glob
+
+import logging
+log = logging.getLogger( __name__ )
+
+def build_ctb_gene(output_file1, output_dir, input_file, mount_point ):
+    #cmdline_str = "build_ctb_gene goterms ${}".format(input_file)
+    cmdline_str = "echo goterms"
+    build_ctb = False
+    try:
+        os.system(cmdline_str)
+        build_ctb = True
+    except:
+        log.debug("Error running the build_ctb_gene goterms", file=sys.stderr)
+
+    # Read the files at the mount point and load the html file
+    if build_ctb == True:
+         files=glob.glob(mount_point)
+         output_file1 = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+                <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+                <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+                <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
+                <title></title>
+                <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+                </head>
+                <body>
+                <div class="toolFormBody">
+                <table>
+                    <th>Files</th>
+                """
+         for file in files:
+             output_file1 += """<tr><td>file</td></tr>"""
+         output_file1 += """</table></div></body></html>\n"""
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool")
+    parser.add_argument('output_file1')
+    parser.add_argument('output_dir')
+    parser.add_argument('--input_file')
+    parser.add_argument('--mount_point')
+    parser.add_argument('--username')
+    parser.add_argument('--password')
+    parser.add_argument('--url')
+    parser.add_argument('--port')
+    args = parser.parse_args()
+
+    export_cmd = "export NEO4J_REST_URL=http://${neo4j_db_username}:${neo4j_db_password}@${neo4j_db_url}:${neo4j_db_port}/db/data/"
+    try:
+        os.system(export_cmd)
+    except:
+        log.debug("Error exporting the NEO4J db environmental values")
+
+    build_ctb_gene(args.output_file1, args.output_dir, args.input_file, args.mount_point)
+
+if __name__ == "__main__": main()
--- a/build_ctb_gene.xml	Tue May 10 14:55:23 2016 -0400
+++ b/build_ctb_gene.xml	Mon May 16 04:20:19 2016 -0400
@@ -1,26 +1,63 @@
 <?xml version="1.0" encoding="utf-8" ?>
 <tool id="build_ctb_gene" name="Build_ctb_gene Tool" version="1.0">
     <requirements>
-       <requirement type="package" version="0.1">build_ctb_gene</requirement>
+       <requirement type="package" version="0.1">build_ctb_gene_neo4j</requirement>
     </requirements>
     <description> build_ctb_gene is the tool used to extract data about genes using locus_tags </description>
     <stdio>
         <exit_code range=":-1" />
         <exit_code range="1:" />
     </stdio>
-    <command>
-        export NEO4J_REST_URL=http://${neo4j_db_username}:${neo4j_db_password}@${neo4j_db_url}:${neo4j_db_port}/db/data/ &amp;&amp;
-        build_ctb_gene goterms ${input_file}
+    <command interpreter="python">
+        build_ctb_gene.py '${outputFile1}' --outputdir ${outputFile2.files_path} --input_file ${input_file} --mount_point ${neo4j_data_mount_point} \
+                            --username ${neo4j_db_username} --password ${neo4j_db_password} --url ${neo4j_db_url} --port ${neo4j_db_port}
     </command>
     <inputs>
         <param name="input_file" type="data" format="gff" label="Choose the GFF file" help="Specify the GFF file" optional="False" />
-        <param type="text" name="neo4j_db_url" value="" label="Neo4j database URL" optional="False" />
-        <param type="text" name="neo4j_db_port" value="" label="Neo4j database port" optional="False" />
-        <param type="text" name="neo4j_db_username" value="" label="Neo4j database username" optional="False" />
-        <param type="text" name="neo4j_db_password" value="" label="Neo4j database password" optional="False" />
+        <param type="text" name="neo4j_data_mount_point" value="" label="Neo4j data mount point" place-holder="/mnt/neo4j/data/lib" optional="False" />
+        <section name="db_settings" title="Neo4j Backend Database Settings" expanded="True">
+            <param type="text" name="neo4j_db_url" value="" label="Neo4j database URL" optional="False" />
+            <param type="text" name="neo4j_db_port" value="" label="Neo4j database port" optional="False" />
+            <param type="text" name="neo4j_db_username" value="" label="Neo4j database username" optional="False" />
+            <param type="text" name="neo4j_db_password" value="" label="Neo4j database password" optional="False" />
+        </section>
     </inputs>
     <outputs>
-        <data format="txt" name="out_file" />
+        <data format="neo4j" name="outputFile1"/>
+        <data format="neostore" name="outputFile2"/>
+        <!--<data format="neostore" name="outputFile3"/>
+        <data format="neostore" name="outputFile4"/>
+        <data format="neostore" name="outputFile5"/>
+        <data format="neostore" name="outputFile6"/>
+        <data format="neostore" name="outputFile7"/>
+        <data format="neostore" name="outputFile8"/>
+        <data format="neostore" name="outputFile9"/>
+        <data format="neostore" name="outputFile10"/>
+        <data format="neostore" name="outputFile11"/>
+        <data format="neostore" name="outputFile12"/>
+        <data format="neostore" name="outputFile13"/>
+        <data format="neostore" name="outputFile14"/>
+        <data format="neostore" name="outputFile15"/>
+        <data format="neostore" name="outputFile16"/>
+        <data format="neostore" name="outputFile17"/>
+        <data format="neostore" name="outputFile18"/>
+        <data format="neostore" name="outputFile19"/>
+        <data format="neostore" name="outputFile20"/>
+        <data format="neostore" name="outputFile21"/>
+        <data format="neostore" name="outputFile22"/>
+        <data format="neostore" name="outputFile23"/>
+        <data format="neostore" name="outputFile24"/>
+        <data format="neostore" name="outputFile25"/>
+        <data format="neostore" name="outputFile26"/>
+        <data format="neostore" name="outputFile27"/>
+        <data format="neostore" name="outputFile28"/>
+        <data format="neostore" name="outputFile29"/>
+        <data format="neostore" name="outputFile30"/>
+        <data format="neostore" name="outputFile31"/>
+        <data format="neostore" name="outputFile32"/>
+        <data format="neostore" name="outputFile33"/>
+        <data format="neostore" name="outputFile34"/>
+        <data format="neostore" name="outputFile35"/> -->
     </outputs>
     <help>Help!</help>
     <citations>