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comparison awkscript.xml @ 0:7222917a3948 draft

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
author brinkmanlab
date Fri, 24 Jan 2020 17:30:15 -0500
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-1:000000000000 0:7222917a3948
1 <tool id="awkscript" name="AWK Script" version="1.0">
2 <description>Transform, modify, or generate data</description>
3 <edam_topics>
4 <edam_topic>topic_0769</edam_topic>
5 </edam_topics>
6 <edam_operations>
7 <edam_operation>operation_3429</edam_operation>
8 <edam_operation>operation_3778</edam_operation>
9 <edam_operation>operation_3434</edam_operation>
10 <edam_operation>operation_2409</edam_operation>
11 </edam_operations>
12 <requirements>
13 <requirement type="package" version="5.0.1">gawk</requirement>
14 </requirements>
15 <version_command>awk --version | head -n 1</version_command>
16 <command><![CDATA[
17 #set $tool_input = 0
18 env -i
19 #for env in $envs
20 '$env.name'='$env.val'
21 #end for
22 awk
23 --sandbox
24 -v FS=' '
25 -v OFS=' '
26 -f '$awk_script'
27 #for group in $infiles
28 tool_input=$tool_input
29 #set $tool_input+=1
30 #if $group.input_type_selection.multiple
31 #set $inputs = $group.input_type_selection.infile
32 ## Allow capturing the collection id in the program
33 ## tool_input_id='$inputs.element_identifier' FIXME collections dont expose their label to tools.
34 #else
35 #set $inputs = [$group.input_type_selection.infile]
36 #end if
37 #for file in $inputs
38 tool_input_id='$file.element_identifier'
39 '$file'
40 #end for
41 #end for
42 > '$outfile'
43 ]]></command>
44 <configfiles>
45 <configfile name="awk_script">$code</configfile>
46 </configfiles>
47 <inputs>
48 <repeat name="infiles" title="Inputs">
49 <conditional name="input_type_selection">
50 <param name="multiple" type="boolean" checked="false" label="Accept multiple" />
51 <when value="false">
52 <param name="infile" format="txt" type="data" label="Single file to process" help="A separate execution will occur for each provided file"/>
53 </when>
54 <when value="true">
55 <param name="infile" format="txt" type="data" multiple="true" label="File or collection to process" />
56 </when>
57 </conditional>
58 </repeat>
59 <param name="code" type="text" area="true" size="5x35" label="AWK Program" help="">
60 <sanitizer sanitize="false" />
61 </param>
62 <repeat name="envs" title="Environment Variables">
63 <param name="name" type="text" label="Name">
64 <sanitizer>
65 <valid initial="string.printable">
66 <remove value="&apos;" />
67 </valid>
68 </sanitizer>
69 </param>
70 <param name="val" type="text" label="Value">
71 <sanitizer>
72 <valid initial="string.printable">
73 <remove value="&apos;" />
74 </valid>
75 </sanitizer>
76 </param>
77 </repeat>
78 </inputs>
79 <outputs>
80 <data name="outfile" format="txt" />
81 </outputs>
82 <tests>
83 <test>
84 <repeat name="envs">
85 <param name="name" value="message" />
86 <param name="val" value="Success!" />
87 </repeat>
88 <param name="code" value="BEGIN { print ENVIRON[&quot;message&quot;]; }" />
89 <output name="outfile">
90 <assert_contents>
91 <has_text text="Success!" />
92 </assert_contents>
93 </output>
94 </test>
95 </tests>
96 <help><![CDATA[
97 GNU AWK Script
98
99 Several kinds of tasks occur repeatedly when working with text files.
100 You might want to extract certain lines and discard the rest. Or you may need to make changes wherever
101 certain patterns appear, but leave the rest of the file alone. Such jobs are often easy with awk.
102 The awk utility interprets a special-purpose programming language that makes it easy to handle simple data-reformatting jobs.
103
104 Each input can be set to single, causing any input collections to map over the tool running, a new instance for each.
105 Setting the input to multiple will pass the entire collection to a single instance of the tool, allowing aggregation of the input data.
106 A mixture of single and multiple inputs is allowed, the single inputs being mapped over and the multiple inputs passed to each instance.
107 This tool is also able to operate with no inputs, generating data for whatever purpose.
108
109 See [GNU AWK Users Guide](https://www.gnu.org/software/gawk/manual/gawk.html) for more information.
110
111 A variable 'tool_input' will be set to the index of the inputs, in order.
112 You can combine this with ARGIND to determine which file you are currently operating on and its position in any possible input collection.
113 A variable 'tool_input_id' is also set specifying the current inputs dataset name or collection id.
114 Beware that ARGIND will increment 3 between inputs as one is consumed setting tool_input and another setting tool_input_id.
115
116 The environment inputs allow you to generalise your scripts, specifying constants with the tool invocation, or allow attaching simple workflow inputs.
117 Environment variables are accessible via [ENVIRON](https://www.gnu.org/software/gawk/manual/gawk.html#index-environment-variables_002c-in-ENVIRON-array).
118
119 Due to a limitation in Galaxy, all output is assigned the 'txt' type. This can be changed in the tool settings in a workflow or modifying the dataset after invocation.
120
121 gawk is run with the [sandbox](https://www.gnu.org/software/gawk/manual/gawk.html#index-sandbox-mode) argument, disabling some functionality.
122 ]]></help>
123 <citations>
124 <citation type="doi">10.5281/zenodo.3364789</citation>
125 </citations>
126 </tool>