diff strip-it.xml @ 0:fc8d71a0fb9b draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/strip-it.xml	Mon May 22 03:01:21 2017 -0400
@@ -0,0 +1,102 @@
+<tool id="ctb_stripit" name="Strip-it" version="1.0.2.1">
+    <description>extracts predefined scaffolds from molecules</description>
+    <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1000" shared_inputs="" merge_outputs="outfile"></parallelism-->
+    <requirements>
+        <requirement type="package" version="1.0.2">strip_it</requirement>
+    </requirements>
+    <command detect_errors="aggressive">
+<![CDATA[
+        ln -s '$infile' '$infile.${infile.ext}' &&
+        strip-it
+            --input '$infile.${infile.ext}'
+            --output '$outfile'
+            --noLog
+            $noHeader
+]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format='sdf,mol,mol2,smi' label="Molecule file" />
+        <param argument='--noHeader' type='boolean' truevalue='--noHeader' falsevalue=''
+            label='Do not print a header in the output file' />
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="sdf" value="CID_3037.sdf"/>
+            <param name="noHeader" value="false"/>
+            <output name="outfile" file="Strip-it_on_CID3037.tabular" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+
+.. class:: infomark
+
+**What this tool does**
+
+Strip-it is a program that extracts predefined scaffolds from organic small
+molecules.
+
+The program comes with a number of predefined molecular scaffolds for
+extraction. These scaffolds include, amongst others
+
+    - `molecular frameworks`_ as originally described by Bemis and Murcko
+    - `molecular frameworks and the reduced molecular frameworks`_ as described by Ansgar Schuffenhauer and coworkers
+    - `scaffold topologies`_ as described by Sara Pollock and coworkers
+
+.. _molecular frameworks: http://www.ncbi.nlm.nih.gov/pubmed/8709122
+.. _molecular frameworks and the reduced molecular frameworks: http://peter-ertl.com/reprints/Schuffenhauer-JCIM-47-47-2007.pdf
+.. _scaffold topologies: http://www.ncbi.nlm.nih.gov/pubmed/18605680
+
+-----
+
+.. class:: infomark
+
+
+**Input**
+
+| - `SD-Format`_
+| - `SMILES Format`_
+| - `MOL2 Format`_
+
+.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
+.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
+.. _MOL2 Format: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
+
+
+-----
+
+.. class:: infomark
+
+**Output**
+
++-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
+|     NAME    |            MOLECULE            | RINGS_WITH_LINKERS_1 |  RINGS_WITH_LINKERS_2  |       MURCKO_1       | ... |
++=============+================================+======================+========================+======================+=====+
+|  Diclofenac | OC(=O)Cc1ccccc1Nc1c(Cl)cccc1Cl | c1ccc(cc1)Nc1ccccc1  |   c1ccc(cc1)Nc1ccccc1  |  C1CCC(CC1)CC1CCCCC1 | ... |
++-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
+| Bupivacaine | CCCCN1CCCCC1C(=O)Nc1c(C)cccc1C | C1CCC(NC1)CNc1ccccc1 | O=C(C1CCCCN1)Nc1ccccc1 | C1CCC(CC1)CCC1CCCCC1 | ... |
++-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
+|     ...     |              ...               |         ...          |           ...          |          ...         | ... |
++-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
+
+-----
+
+.. class:: infomark
+
+**Cite**
+
+`Silicos-it`_ - strip-it
+
+.. _Silicos-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/strip-it/1.0.2/strip-it.html
+
+
+]]>
+    </help>
+    <citations>
+    </citations>
+</tool>