Mercurial > repos > bgruening > scipy_sparse

annotate sparse.xml @ 37:803df7662b9e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
author bgruening
date Wed, 22 Jan 2020 12:29:51 +0000
parents 0d9666476157
children 2702bc38f946
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
1 <tool id="scipy_sparse" name="Sparse Matrix Functions" version="@VERSION@">
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
2 <description>for manipulating 2-D Scipy sparse numeric data</description>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
3 <macros>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
4 <import>main_macros.xml</import>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
5 </macros>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
6 <expand macro="python_requirements"/>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
7 <expand macro="macro_stdio"/>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
8 <version_command>echo "@VERSION@"</version_command>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
9 <command>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
10 <![CDATA[
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
11 python "$sparse_script" '$inputs'
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
12 ]]>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
13 </command>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
14 <configfiles>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
15 <inputs name="inputs" />
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
16 <configfile name="sparse_script">
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
17 <![CDATA[
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
18 import sys
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
19 import json
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
20 import pandas
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
21 import numpy as np
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
22 from scipy import sparse
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
23 from scipy.io import mmread
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
24 from scipy.io import mmwrite
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
25
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
26 input_json_path = sys.argv[1]
20
01c0f1b60556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 1
diff changeset
27 with open(input_json_path, "r") as param_handler:
01c0f1b60556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 1
diff changeset
28 params = json.load(param_handler)
0
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
29
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
30 sparse_iter = []
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
31 #for $i, $s in enumerate( $sparse_functions.sparse_inputs )
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
32 sparse_index=$i
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
33 sparse_path="${s.input.file_name}"
20
01c0f1b60556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 1
diff changeset
34 sparse_iter.append(mmread(sparse_path))
0
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
35 #end for
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
36
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
37 my_function = getattr(sparse, params["sparse_functions"]["selected_function"])
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
38 my_sparse = my_function(sparse_iter)
26
0d9666476157 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 20
diff changeset
39 with open("$outfile", "wb") as out_handler:
20
01c0f1b60556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 1
diff changeset
40 mmwrite(out_handler, my_sparse)
0
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
41 ]]>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
42 </configfile>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
43 </configfiles>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
44 <inputs>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
45 <conditional name="sparse_functions">
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
46 <param name="selected_function" type="select" label="Select a task:">
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
47 <option value="vstack" selected="true">Stack sparse matrices vertically (vstack)</option>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
48 <option value="hstack">Stack sparse matrices horizontally (hstack)</option>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
49 </param>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
50 <when value="vstack">
1
1191a102a5c1 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
51 <expand macro="multiple_input" name="sparse_inputs"/>
0
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
52 </when>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
53 <when value="hstack">
1
1191a102a5c1 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
54 <expand macro="multiple_input" name="sparse_inputs"/>
0
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
55 </when>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
56 </conditional>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
57 </inputs>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
58 <outputs>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
59 <data format="txt" name="outfile"/>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
60 </outputs>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
61 <tests>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
62 <test>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
63 <param name="selected_function" value="vstack"/>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
64 <param name="sparse_inputs_0|input" value="csr_sparse1.mtx" ftype="txt"/>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
65 <param name="sparse_inputs_1|input" value="csr_sparse2.mtx" ftype="txt"/>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
66 <output name="outfile" file="csr_stack_result01.mtx"/>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
67 </test>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
68 <test>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
69 <param name="selected_function" value="hstack"/>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
70 <param name="sparse_inputs_0|input" value="csc_sparse1.mtx" ftype="txt"/>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
71 <param name="sparse_inputs_1|input" value="csc_sparse2.mtx" ftype="txt"/>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
72 <output name="outfile" file="csc_stack_result01.mtx"/>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
73 </test>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
74 </tests>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
75 <help>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
76 <![CDATA[
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
77 **What it does**
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
78
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
79 This tool stacks sparse matrices horizontally (column wise) or vertically (row wise).
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
80 It can handle two different formats:
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
81
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
82 * Compressed Sparse Column matrix (csc_matrix)
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
83
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
84 * Compressed Sparse Row matrix (csr_matrix)
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
85
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
86 Sparse matrices in column format should be stacked horizontally (hstack) , while matrices in row format are stacked vertically (vstack). This tool outputs a single resulting sparse matrix which is compatible with the inputs in format.
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
87
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
88 **Parameters:** blocks sequence of sparse matrices with compatible shapes format.
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
89
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
90 For more information please refer to DOI:10.1109/MCSE.2011.37.
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
91 ]]>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
92 </help>
25b93d50158f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
93 <expand macro="scipy_citation"/>
26
0d9666476157 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 20
diff changeset
94 </tool>