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1 | | -#download_from_gdc |
2 | | -#Tue Feb 06 20:14:16 UTC 2018 |
| 1 | +#ABasicModule |
| 2 | +#Tue May 01 20:52:13 UTC 2018 |
3 | 3 | JVMLevel= |
4 | | -LSID=urn\:lsid\:broad.mit.edu\:cancer.software.genepattern.module.analysis\:00369\:2.3 |
5 | | -author=Edwin F. Juarez & Andy Zhang;UCSD -- Mesirov Lab |
6 | | -categories=Data Format Conversion |
7 | | -commandLine=<python_3.6> <libdir>download_from_manifest.py -m <manifest> -n <metadata> -o <output_file_name> -g <gct> -t <translate_gene_id> -c <cls> |
8 | | -# This next line "job.docker.image=" is here for future uses, currently it does nothing, we need to ad a tag, e.g., "job.docker.image=genepattern/download_from_gdc:1.0.0" |
9 | | -job.docker.image=genepattern/download_from_gdc:0.1 |
| 4 | +LSID=urn\:lsid\:8080.gpserver.ip-172-31-26-71.ip-172-31-26-71.ec2.internal\:genepatternmodules\:42\:4 |
| 5 | +author=Edwin F. Juarez;UCSD - Mesirov Lab |
| 6 | +categories=Administration |
| 7 | +commandLine=<python_3.6> <libdir>ABasicModule.py -f <filename> -a <add_custom_message> -m <message_to_add> -o <output_filename> |
| 8 | +job.docker.image=genepattern/docker-python36:0.4 |
10 | 9 | cpuType=any |
11 | | -description=This module takes in a GDC manifest file, download the files listed on that manifest, and renames them to be human-friendly. |
12 | | -fileFormat=counts;gct;txt |
| 10 | +description=This is a basic GenePattern module written in Python 3. It can be taken as a "blank canvas" for future modules. It reads a file and potentially adds a |
| 11 | +fileFormat=txt |
13 | 12 | language=Python |
14 | | -name=download_from_gdc |
| 13 | +name=ABasicModule |
15 | 14 | os=any |
16 | 15 | p1_MODE=IN |
17 | 16 | p1_TYPE=FILE |
18 | 17 | p1_default_value= |
19 | | -p1_description=The relative path of the manifest used to download the data. This file is obtained from the GDC data portal (https://portal.gdc.cancer.gov/). |
| 18 | +p1_description=Name of the file to be read |
20 | 19 | p1_fileFormat=txt |
21 | | -p1_flag=-m |
22 | | -p1_name=manifest |
| 20 | +p1_flag=-f |
| 21 | +p1_name=filename |
23 | 22 | p1_numValues=0..1 |
24 | 23 | p1_optional= |
25 | 24 | p1_prefix= |
26 | 25 | p1_prefix_when_specified= |
27 | 26 | p1_type=java.io.File |
28 | 27 | p1_value= |
29 | | -p2_MODE=IN |
30 | | -p2_TYPE=FILE |
31 | | -p2_default_value= |
32 | | -p2_description=The relative path of the metadata file. |
33 | | -p2_fileFormat=json |
34 | | -p2_flag=-n |
35 | | -p2_name=metadata |
| 28 | +p2_MODE= |
| 29 | +p2_TYPE=TEXT |
| 30 | +p2_default_value=False |
| 31 | +p2_description=Wether or not to add a custom message |
| 32 | +p2_fileFormat= |
| 33 | +p2_flag=-a |
| 34 | +p2_name=add_custom_message |
36 | 35 | p2_numValues=0..1 |
37 | 36 | p2_optional= |
38 | 37 | p2_prefix= |
39 | 38 | p2_prefix_when_specified= |
40 | | -p2_type=java.io.File |
41 | | -p2_value= |
| 39 | +p2_type=java.lang.String |
| 40 | +p2_value=False\=False;True\=True |
42 | 41 | p3_MODE= |
43 | 42 | p3_TYPE=TEXT |
44 | | -p3_default_value=TCGA_dataset |
45 | | -p3_description=The base name to use for output files. E.g., if you type "TCGA_dataset" then the GCT file will be named "TCGA_dataset.gct" |
| 43 | +p3_default_value= |
| 44 | +p3_description=What message to add (if any) |
46 | 45 | p3_fileFormat= |
47 | | -p3_flag=-o |
48 | | -p3_name=output_file_name |
| 46 | +p3_flag=-m |
| 47 | +p3_name=message_to_add |
49 | 48 | p3_numValues=0..1 |
50 | | -p3_optional=on |
| 49 | +p3_optional= |
51 | 50 | p3_prefix= |
52 | 51 | p3_prefix_when_specified= |
53 | 52 | p3_type=java.lang.String |
54 | 53 | p3_value= |
55 | 54 | p4_MODE= |
56 | 55 | p4_TYPE=TEXT |
57 | | -p4_default_value=True |
58 | | -p4_description=whether or not to create a gct file |
| 56 | +p4_default_value= |
| 57 | +p4_description=The basename to use for output file (no need to add ".txt" at the end) |
59 | 58 | p4_fileFormat= |
60 | | -p4_flag=-g |
61 | | -p4_name=gct |
| 59 | +p4_flag=-o |
| 60 | +p4_name=output_filename |
62 | 61 | p4_numValues=0..1 |
63 | 62 | p4_optional= |
64 | 63 | p4_prefix= |
65 | 64 | p4_prefix_when_specified= |
66 | 65 | p4_type=java.lang.String |
67 | | -p4_value=True\=True;False\=False |
68 | | -p5_MODE= |
69 | | -p5_TYPE=TEXT |
70 | | -p5_default_value=False |
71 | | -p5_description=Whether or not to translate ENSEMBL IDs (e.g., ENSG00000012048) to Hugo Gene Symbol (e.g., BRCA1) |
72 | | -p5_fileFormat= |
73 | | -p5_flag=-t |
74 | | -p5_name=translate_gene_id |
75 | | -p5_numValues=0..1 |
76 | | -p5_optional= |
77 | | -p5_prefix= |
78 | | -p5_prefix_when_specified= |
79 | | -p5_type=java.lang.String |
80 | | -p5_value=False\=False;True\=True |
81 | | -p6_default_value=True |
82 | | -p6_description=Whether or not to translate create a cls file separating Normal and Tumor classes based on TCGA Sample ID. |
83 | | -p6_fileFormat= |
84 | | -p6_flag=-c |
85 | | -p6_name=cls |
86 | | -p6_numValues=0..1 |
87 | | -p6_optional= |
88 | | -p6_prefix= |
89 | | -p6_prefix_when_specified= |
90 | | -p6_type=java.lang.String |
91 | | -p6_value=False\=False;True\=True |
| 66 | +p4_value= |
92 | 67 | privacy=public |
93 | 68 | quality=production |
94 | | -taskDoc=doc.html |
95 | | -taskType=Data Format Conversion |
| 69 | +taskDoc= |
| 70 | +taskType=Administration |
96 | 71 | userid=edjuaro |
97 | | -version=Initial version++ |
| 72 | +version=Initial version |
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