diff sdf2fps.xml @ 2:70b071de9bee draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sdf2fps.xml	Sat May 20 08:31:44 2017 -0400
@@ -0,0 +1,116 @@
+<tool id="ctb_sdf2fps" name="SDF to Fingerprint" version="0.2">
+    <description>extract fingerprints from sdf files metadata</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="1.1p1">chemfp</requirement>
+        <requirement type="package" version="2.4.1">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        sdf2fps --pubchem '${infile}' > '${outfile}'
+]]>
+    </command>
+    <inputs>
+        <param name="infile" type='data' format="sdf" label="SDF file with fingerprints as metadata"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="fps"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="sdf" value="CID_2244.sdf" />
+            <output name="outfile" file='sdf2fps_result1.fps' ftype="fps" lines_diff="4" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+Read an input SD file, extract the fingerprints and store them in a FPS-file.
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+`SD-Format`_
+
+.. _`SD-Format`: http://en.wikipedia.org/wiki/Chemical_table_file
+
+* Example::
+
+		28434379
+		  -OEChem-02031205132D
+
+		 37 39  0     0  0  0  0  0  0999 V2000
+		    8.1648   -1.8842    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+		    6.0812   -0.2134    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+		    6.0812   -1.8229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+		    2.5369   -2.0182    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+		    6.3919    0.7371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+		    7.3704    0.9433    0.0000 C   0  0  0  0
+		    ......
+		  1 15  1  0  0  0  0
+		  1 35  1  0  0  0  0
+		  2  5  1  0  0  0  0
+		  2 11  1  0  0  0  0
+		  2 12  1  0  0  0  0
+		  3 12  2  0  0  0  0
+		  3 13  1  0  0  0  0
+		  4 18  1  0  0  0  0
+		  ......
+
+			>PUBCHEM_COMPOUND_CID<
+			28434379
+
+			> <PUBCHEM_COMPOUND_CANONICALIZED>
+			1
+
+			> <PUBCHEM_CACTVS_COMPLEXITY>
+			280
+
+			> <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
+			2
+
+			> <PUBCHEM_CACTVS_HBOND_DONOR>
+			2
+
+			> <PUBCHEM_CACTVS_ROTATABLE_BOND>
+			2
+
+			> <PUBCHEM_CACTVS_SUBSKEYS>
+			AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
+
+			>
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+* Example::
+
+	#FPS1
+	#num_bits=881
+	#type=CACTVS-E_SCREEN/1.0 extended=2
+	#software=CACTVS/unknown
+	#source=/home/mohammed/galaxy-central/database/files/000/dataset_409.dat
+	#date=2012-02-03T10:44:12
+	07ce04000000000000000000000000000080060000000c0600
+	00000000001a800f0000780008100000101487e9608c0bed32
+	48000580644626204101b4844805901b041c2e19511e45039b
+	8b2924101609401b13e4080000000000010020000004008000
+	0010000002000000000000	28434379
+
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1186/1758-2946-5-S1-P36</citation>
+    </citations>
+</tool>