diff modify/change_title_to_metadata_value.xml @ 0:527ecd2fc500 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/modify/change_title_to_metadata_value.xml	Thu Aug 15 03:25:06 2013 -0400
@@ -0,0 +1,64 @@
+<tool id="ctb_change_title" name="Change Title" version="0.0.1">
+    <description>to meta-data value.</description>
+    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command interpreter="python">
+        ## The command is a Cheetah template which allows some Python based syntax.
+        ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
+        change_title_to_metadata_value.py
+        --infile "${infile}"
+        --key "${key}"
+        --outfile "${outfile}"
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="sdf,mol2" label="Compound File" help="Specify a compound file in SD- or MOL2-format."/>
+        <param name="key" type="text" format="text" label="Compound Identifier encoded in the SDF file." help="Specify the key name of the SDF metadata, that contains the molecule identifier."/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format_source="infile"/>
+    </outputs>
+    <tests>
+        <param name="infile" type="sdf" value="CID_3033.sdf"/>
+        <param name="key" value="PUBCHEM_SHAPE_VOLUME"/>
+        <data name="output" type="sdf" file="change_title_on_CID_3033.sdf"/>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**What this tool does**
+
+Changes the title of a molecule file to a metadata value of a given ID in the same molecule file.
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+`SD-file`_ with metadata including the given ID.
+
+.. _SD-file: http://en.wikipedia.org/wiki/Chemical_table_file
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+Same as input with changed title tag.
+
+-----
+
+.. class:: infomark
+
+**Cite**
+
+`Open Babel`_
+
+.. _Open Babel: http://openbabel.org/wiki/Main_Page
+
+    </help>
+</tool>