changeset 0:fc8d71a0fb9b draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
author bgruening
date Mon, 22 May 2017 03:01:21 -0400
parents
children b8809b15e1a4
files strip-it.xml test-data/CID_3037.sdf test-data/Strip-it_on_CID3037.tabular
diffstat 3 files changed, 324 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CID_3037.sdf	Mon May 22 03:01:21 2017 -0400
@@ -0,0 +1,220 @@
+3037
+  -OEChem-08231108593D
+
+ 27 28  0     0  0  0  0  0  0999 V2000
+   -4.8550    1.3401    0.2120 Cl  0  0  0  0  0  0  0  0  0  0  0  0
+    4.8529   -1.3406    0.2121 Cl  0  0  0  0  0  0  0  0  0  0  0  0
+   -0.1809   -2.1668   -0.3789 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.1788    2.1664   -0.3787 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.0011   -0.0002    1.4744 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2222   -0.2738    0.6597 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2377    0.2772    0.6480 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2586   -1.3462   -0.2316 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2565    1.3457   -0.2314 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.3343    0.5568    0.7972 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.3322   -0.5574    0.7972 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.4069   -1.5879   -0.9855 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4048    1.5875   -0.9852 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.4827    0.3152    0.0433 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.4807   -0.3156    0.0435 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.5190   -0.7571   -0.8481 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.5170    0.7568   -0.8478 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.1548    0.8649    2.1342 H   0  0  0  0  0  0  0  0  0  0  0  0
+    0.1601   -0.8435    2.1593 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.3089    1.3938    1.4913 H   0  0  0  0  0  0  0  0  0  0  0  0
+    2.3053   -1.3909    1.4943 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.4415   -2.4213   -1.6818 H   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4469    2.4191   -1.6835 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.4070   -0.9574   -1.4422 H   0  0  0  0  0  0  0  0  0  0  0  0
+    4.4050    0.9570   -1.4418 H   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2961   -2.2262    0.4641 H   0  0  0  0  0  0  0  0  0  0  0  0
+    0.3872    2.8487   -1.0397 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1 14  1  0  0  0  0
+  2 15  1  0  0  0  0
+  3  8  1  0  0  0  0
+  3 26  1  0  0  0  0
+  4  9  1  0  0  0  0
+  4 27  1  0  0  0  0
+  5  6  1  0  0  0  0
+  5  7  1  0  0  0  0
+  5 18  1  0  0  0  0
+  5 19  1  0  0  0  0
+  6  8  2  0  0  0  0
+  6 10  1  0  0  0  0
+  7  9  2  0  0  0  0
+  7 11  1  0  0  0  0
+  8 12  1  0  0  0  0
+  9 13  1  0  0  0  0
+ 10 14  2  0  0  0  0
+ 10 20  1  0  0  0  0
+ 11 15  2  0  0  0  0
+ 11 21  1  0  0  0  0
+ 12 16  2  0  0  0  0
+ 12 22  1  0  0  0  0
+ 13 17  2  0  0  0  0
+ 13 23  1  0  0  0  0
+ 14 16  1  0  0  0  0
+ 15 17  1  0  0  0  0
+ 16 24  1  0  0  0  0
+ 17 25  1  0  0  0  0
+M  END
+> <PUBCHEM_COMPOUND_CID>
+3037
+
+> <PUBCHEM_CONFORMER_RMSD>
+0.6
+
+> <PUBCHEM_CONFORMER_DIVERSEORDER>
+8
+10
+12
+1
+7
+5
+11
+3
+6
+9
+4
+2
+
+> <PUBCHEM_MMFF94_PARTIAL_CHARGES>
+25
+1 -0.18
+10 -0.15
+11 -0.15
+12 -0.15
+13 -0.15
+14 0.18
+15 0.18
+16 -0.15
+17 -0.15
+2 -0.18
+20 0.15
+21 0.15
+22 0.15
+23 0.15
+24 0.15
+25 0.15
+26 0.45
+27 0.45
+3 -0.53
+4 -0.53
+5 0.29
+6 -0.14
+7 -0.14
+8 0.08
+9 0.08
+
+> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>
+2
+
+> <PUBCHEM_PHARMACOPHORE_FEATURES>
+4
+1 3 donor
+1 4 donor
+6 6 8 10 12 14 16 rings
+6 7 9 11 13 15 17 rings
+
+> <PUBCHEM_HEAVY_ATOM_COUNT>
+17
+
+> <PUBCHEM_ATOM_DEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_BOND_DEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_BOND_UDEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_ISOTOPIC_ATOM_COUNT>
+0
+
+> <PUBCHEM_COMPONENT_COUNT>
+1
+
+> <PUBCHEM_CACTVS_TAUTO_COUNT>
+5
+
+> <PUBCHEM_CONFORMER_ID>
+00000BDD00000008
+
+> <PUBCHEM_MMFF94_ENERGY>
+44.6858
+
+> <PUBCHEM_FEATURE_SELFOVERLAP>
+20.297
+
+> <PUBCHEM_SHAPE_FINGERPRINT>
+10062212 137 18261117369936506423
+104564 63 17986963035811110412
+11458722 120 18339359768245870841
+11471102 22 5472872458301843344
+11578080 2 18190204380446433792
+116883 192 18265608969609498196
+12236239 1 18410856576819659107
+12592029 89 18338223951597366363
+13549 16 18410575084668353682
+13693222 15 6555421915516066822
+13764800 53 14189033175566991199
+14115302 16 18186237320680093898
+14341114 328 10087642619424135543
+14787075 74 9511159855286719151
+14993402 34 18410855451538227223
+15099037 51 18340768233908588503
+15207287 21 15719111361650760302
+15375358 24 15647053767618106914
+15775835 57 18272650117329930317
+16945 1 17906452130063974618
+17834072 14 15936410035134206066
+18186145 218 17132117918276567720
+19422 9 18271525295227750719
+20279233 1 15719389529571237654
+20645476 183 18339080393619327415
+23402539 116 18186809105365620101
+23402655 69 18342736308283284156
+23559900 14 17603590712323212176
+25 1 17561083592297532664
+26918003 58 6266902359448424189
+296302 2 15213020427345972082
+3082319 5 18338798905472319583
+34934 24 18341891845236497020
+633830 44 17703790310130762689
+74978 22 18266740181857992718
+7832392 63 18340206284835898173
+81228 2 15720767252053392762
+9981440 41 17403743242177431832
+
+> <PUBCHEM_SHAPE_MULTIPOLES>
+341.85
+8.38
+1.9
+1.1
+0.02
+0
+-1.15
+1.94
+-0.01
+0
+-0.39
+-4.15
+0.01
+0
+
+> <PUBCHEM_SHAPE_SELFOVERLAP>
+722.787
+
+> <PUBCHEM_SHAPE_VOLUME>
+193
+
+> <PUBCHEM_COORDINATE_TYPE>
+2
+5
+255
+
+$$$$
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Strip-it_on_CID3037.tabular	Mon May 22 03:01:21 2017 -0400
@@ -0,0 +1,2 @@
+NAME	MOLECULE	RINGS_WITH_LINKERS_1	RINGS_WITH_LINKERS_2	MURCKO_1	MURCKO_2	OPREA_1	OPREA_2	OPREA_3	SCHUFFENHAUER_1	SCHUFFENHAUER_2	SCHUFFENHAUER_3	SCHUFFENHAUER_4	SCHUFFENHAUER_5
+3037	Oc1ccc(cc1Cc1cc(Cl)ccc1O)Cl	c1ccc(cc1)Cc1ccccc1	c1ccc(cc1)Cc1ccccc1	C1CCC(CC1)CC1CCCCC1	C1CCC(CC1)C1CCCCC1	C1CC1C1CC1	C1CC1C1CC1	C1CC1C1CC1	c1ccccc1	c1ccc(cc1)Cc1ccccc1	c1ccc(cc1)Cc1ccccc1	c1ccc(cc1)Cc1ccccc1	c1ccc(cc1)Cc1ccccc1