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comparison macros.xml @ 0:9512201417a5 draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
author mbernt
date Sun, 06 Aug 2023 15:21:11 +0000
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-1:000000000000 0:9512201417a5
1 <macros>
2 <xml name="command_macro">
3 <command detect_errors="aggressive"><![CDATA[
4 #import re
5 mkdir inputs &&
6 #for $p in $parameters
7 #if $p.type_cond.type_sel == "data"
8 #if $p.type_cond.filename != ''
9 #set fname = $p.type_cond.filename
10 #else
11 #set fname=re.sub('[^\s\w\.]', '_', str($p.type_cond.param.element_identifier)) + "." + $p.type_cond.param.ext
12 #end if
13 ln -s '$p.type_cond.param' inputs/'$fname' &&
14 #end if
15 #end for
16
17 @COMMAND_AND_SETUP@
18 '$script'
19 #for $p in $parameters
20 #if $p.type_cond.type_sel == "data"
21 #if $p.type_cond.filename != ''
22 #set fname = $p.type_cond.filename
23 #else
24 #set fname=re.sub('[^\s\w\.]', '_', str($p.type_cond.param.element_identifier)) + "." + $p.type_cond.param.ext
25 #end if
26 inputs/'$fname'
27 #else
28 '$p.type_cond.param'
29 #end if
30 #end for
31 ]]></command>
32 <configfiles>
33 <configfile name="script">$code</configfile>
34 </configfiles>
35 </xml>
36 <xml name="inputs_macro">
37 <inputs>
38 <repeat name="parameters" title="Parameters" min="1" default="1" help="Supply one or more parameters">
39 <conditional name="type_cond">
40 <param name="type_sel" type="select" label="Parameter type">
41 <option value="data">Dataset</option>
42 <option value="text">Text</option>
43 <!-- Not sure if int/float make sense .. can they be connected to text in WFs? -->
44 </param>
45 <when value="data">
46 <param name="param" type="data" label="Dataset"/>
47 <param name="filename" type="text" label="File name" help="Set if you want to access the data set with a specific file name. Only alphanumeric characters, dash and underscore are allowed (all other characters are replaced by an undercore). Default is Galaxy's data set name.">
48 <sanitizer invalid_char="_">
49 <valid initial="string.ascii_letters,string.digits">
50 <add value="_" />
51 <add value="-" />
52 <add value="." />
53 </valid>
54 </sanitizer>
55 <!-- file names must not start with dash -->
56 <validator type="regex" negate="true" message="Filenames must not start with a dash">^[-].*$</validator>
57 </param>
58 </when>
59 <when value="text">
60 <param name="param" type="text" label="Text parameter" help=""/>
61 </when>
62 </conditional>
63 </repeat>
64 <param name="code" type="text" area="true" label="@LANGUAGE@ program" help="">
65 <sanitizer>
66 <valid initial="string.printable"/>
67 </sanitizer>
68 </param>
69 </inputs>
70 </xml>
71 <xml name="outputs_macro">
72 <outputs>
73 <collection name="output" type="list" label="Outputs">
74 <discover_datasets pattern="__designation_and_ext__"/>
75 </collection>
76 </outputs>
77 </xml>
78
79 <xml name="help_macro">
80 <help><![CDATA[
81 **Warning**
82
83 .. class:: warningmark
84
85 **Make sure that you know what you are doing. When used wrong the tool may lead to
86 data loss of files that you can write to.**
87
88 .. class:: warningmark
89
90 This tool is only intended to serve for single-use, ad-hoc exploratory analysis
91 of data sets with small @LANGUAGE@ scripts.
92
93 .. class:: warningmark
94
95 If you use this tool repeatedly with the same script and/or have the impression
96 that other Galaxy users could profit from this script then contact your local
97 Galaxy administrator or the Galaxy community, e.g. at https://github.com/galaxyproject/tools-iuc/,
98 and ask if your script can be turned into a proper Galaxy tool.
99 One of the main advantages of a proper Galaxy tool is that they are tested and
100 maintained. Furthermore the whole Galaxy community may profit.
101
102 **What it does**
103
104 Executes an **@LANGUAGE@** script (in a @CONTAINER@ container).
105
106 An arbitrary number of data or text parameters can be given to the script.
107 Data parameters are by default named like the datasets name and the datatype
108 is used as extension. This can be overwritten with the filename parameter
109 for the corresponding dataset.
110
111 @HELP_PARAMETERS@
112
113 @HELP_READ_FROM_STDIN@
114
115 Output datasets are read from the current working directory and put into a
116 single collection. The collection elements will be named as the file names
117 (without the extension). The file extension determines the datatype of the
118 datasets (or Galaxy will try to autodetect the data type).
119 ]]></help>
120 </xml>
121 </macros>