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comparison interproscan5/ipsfaux.xml @ 3:74cf3f49f10c draft

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Better HTML index.
author mkh
date Tue, 02 Feb 2016 12:27:19 -0500
parents e2d4343d73ad
children 6574eb46426d
comparison
equal deleted inserted replaced
2:d1d34608dba0 3:74cf3f49f10c
1 <tool id="ipsfaux" name="Faux Interproscan" version="1.0.0a"> 1 <tool id="ipsfaux" name="Faux Interproscan" version="1.0.1a">
2 <description>Interproscan functional predictions of ORFs (faux). Input file and computation options are 2 <description>Interproscan functional predictions of ORFs (faux). Input file and computation options are
3 ignored (other than the types of outputs). The same precomputed results are produced every time.</description> 3 ignored (other than the types of outputs). The same precomputed results are produced every time.</description>
4 <requirements> 4 <requirements>
5 <!-- 5 <!--
6 <requirement type="package">signalp</requirement> 6 <requirement type="package">signalp</requirement>
10 <requirement type="set_environment">INTERPROSCAN_SCRIPT_PATH</requirement> 10 <requirement type="set_environment">INTERPROSCAN_SCRIPT_PATH</requirement>
11 </requirements> 11 </requirements>
12 12
13 <command> 13 <command>
14 #import os 14 #import os
15 echo "output_types=$output_types"; 15 echo "Start timestamp: \$(date)";
16
17 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/fake_ips.py 16 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/fake_ips.py
18 ## disables the precalculated lookup service, all calculation will be run locally 17 ## disables the precalculated lookup service, all calculation will be run locally
19 -dp 18 -dp
20 --input $infile 19 --input $infile
21 --seqtype $seqtype 20 --seqtype $seqtype
22 -f $output_types 21 -f $output_types
23 --applications $appl 22 --applications $appl
24 --tempdir \$TEMP
25 23
26 $pathways 24 $pathways
27 $goterms 25 $goterms
28 $iprlookup 26 $iprlookup
29 $mode 27 $mode
30 --output-file-base __base__ 28 --output-file-base __base__
31 2>&#38;1; 29 2>&#38;1;
32 30
33 #if 'tsv' in str($output_types): 31 mv __base__.tsv $tsv_file;
34 mv __base__.tsv $tsv_file;
35 #end if
36 32
37 #if 'gff3' in str($output_types): 33 #if 'gff3' in str($output_types):
38 mv __base__.gff3 $gff3_file; 34 mv __base__.gff3 $gff3_file;
39 #end if 35 #end if
40 36
44 40
45 #if 'html' in str($output_types): 41 #if 'html' in str($output_types):
46 mkdir -p $html_file.files_path; 42 mkdir -p $html_file.files_path;
47 #set temp_archive_file = '__base__.html.tar.gz' 43 #set temp_archive_file = '__base__.html.tar.gz'
48 tar -C $html_file.files_path -xvmzf $temp_archive_file; 44 tar -C $html_file.files_path -xvmzf $temp_archive_file;
49 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $html_file $html_file.files_path; 45 #if str($seqtype) == 'p' and not str($getorfed):
46 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 0 $tsv_file $html_file $html_file.files_path;
47 #else
48 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 1 $tsv_file $html_file $html_file.files_path;
49 #end if
50 rm $temp_archive_file; 50 rm $temp_archive_file;
51 #end if 51 #end if
52 52
53 #if 'svg' in str($output_types): 53 #if 'svg' in str($output_types):
54 mkdir -p $svg_file.files_path; 54 mkdir -p $svg_file.files_path;
55 #set temp_archive_file = '__base__.svg.tar.gz' 55 #set temp_archive_file = '__base__.svg.tar.gz'
56 tar -C $svg_file.files_path -xvmzf $temp_archive_file; 56 tar -C $svg_file.files_path -xvmzf $temp_archive_file;
57 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $svg_file $svg_file.files_path; 57 #if str($seqtype) == 'p' and not str($getorfed):
58 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 0 $tsv_file $svg_file $svg_file.files_path;
59 #else
60 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 1 $tsv_file $svg_file $svg_file.files_path;
61 #end if
58 rm $temp_archive_file; 62 rm $temp_archive_file;
59 #end if 63 #end if
60 64
61 echo "End of ipsfaux" 65 echo "End timestamp: \$(date)"
62 </command> 66 </command>
63 67
64 <inputs> 68 <inputs>
65 <param name="infile" type="data" format="fasta" label="Sequence Fasta File (ignored -- faux mode)"/> 69 <param name="infile" type="data" format="fasta" label="Sequence Fasta File (ignored -- faux mode)"/>
66 70
67 <param name="seqtype" type="select" label="Type of the input sequences" help=""> 71 <param name="seqtype" type="select" label="Type of the input sequences" help="">
68 <option value="p" selected="true">Protein</option> 72 <option value="p" selected="true">Protein</option>
69 <option value="n">DNA / RNA</option> 73 <option value="n">DNA / RNA</option>
70 </param> 74 </param>
75
76 <param name="getorfed" type="boolean" label="DNA/RNA was externally processed by getorf?" help="Ignored for DNA inputs."
77 truevalue="getorfed"
78 falsevalue=""/>
71 79
72 <param name="mode" type="boolean" label="Run on cluster?" help="Check to submit job to cluster." 80 <param name="mode" type="boolean" label="Run on cluster?" help="Check to submit job to cluster."
73 truevalue="--mode=cluster --clusterrunid=gtdi-ips-analysis" 81 truevalue="--mode=cluster --clusterrunid=gtdi-ips-analysis"
74 falsevalue=""/> 82 falsevalue=""/>
75 83
109 117
110 <param name="iprlookup" truevalue="--iprlookup" falsevalue="" checked="False" type="boolean" 118 <param name="iprlookup" truevalue="--iprlookup" falsevalue="" checked="False" type="boolean"
111 label="Provide additional mappings" 119 label="Provide additional mappings"
112 help="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into (--iprlookup)"/> 120 help="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into (--iprlookup)"/>
113 121
114 <param name="output_types" type="select" display="checkboxes" multiple="true" label="Output formats" 122 <param name="output_types" type="select" display="checkboxes" multiple="true" label="Output formats (in addition to TSV)"
115 help="Select the output formats to generate (at least one)"> 123 help="Select the output formats to generate (at least one)">
116 <option value="tsv" selected="true">Raw (TSV)</option>
117 <option value="html" selected="true">HTML (Graphical)</option> 124 <option value="html" selected="true">HTML (Graphical)</option>
118 <option value="svg" selected="false">SVG (Scalable Vector Graphics)</option> 125 <option value="svg" selected="false">SVG (Scalable Vector Graphics)</option>
119 <option value="gff3" selected="true">GFF3</option> 126 <option value="gff3" selected="true">GFF3</option>
120 <option value="xml" selected="false">XML</option> 127 <option value="xml" selected="false">XML</option>
121 </param> 128 </param>
122 </inputs> 129 </inputs>
123 130
124 <outputs> 131 <outputs>
125 <data format="tabular" name="tsv_file" label="Interproscan TSV on ${on_string}"> 132 <data format="tabular" name="tsv_file" label="Interproscan TSV on ${on_string}"/>
126 <filter>'tsv' in output_types</filter>
127 </data>
128 <data format="html" name="html_file" label="Interproscan HTML on ${on_string}"> 133 <data format="html" name="html_file" label="Interproscan HTML on ${on_string}">
129 <filter>'html' in output_types</filter> 134 <filter>'html' in output_types</filter>
130 </data> 135 </data>
131 <data format="html" name="svg_file" label="Interproscan SVG on ${on_string}"> 136 <data format="html" name="svg_file" label="Interproscan SVG on ${on_string}">
132 <filter>'svg' in output_types</filter> 137 <filter>'svg' in output_types</filter>