Mercurial > repos > mbernt > singularity_scriptrunner

annotate macros.xml @ 0:3d41fa089db7 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 15:20:57 +0000
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3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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1 <macros>
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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2 <xml name="command_macro">
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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3 <command detect_errors="aggressive"><![CDATA[
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4 #import re
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5 mkdir inputs &&
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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6 #for $p in $parameters
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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7 #if $p.type_cond.type_sel == "data"
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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8 #if $p.type_cond.filename != ''
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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9 #set fname = $p.type_cond.filename
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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10 #else
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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11 #set fname=re.sub('[^\s\w\.]', '_', str($p.type_cond.param.element_identifier)) + "." + $p.type_cond.param.ext
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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12 #end if
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13 ln -s '$p.type_cond.param' inputs/'$fname' &&
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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14 #end if
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15 #end for
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16
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17 @COMMAND_AND_SETUP@
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18 '$script'
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19 #for $p in $parameters
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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20 #if $p.type_cond.type_sel == "data"
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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21 #if $p.type_cond.filename != ''
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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22 #set fname = $p.type_cond.filename
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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23 #else
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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24 #set fname=re.sub('[^\s\w\.]', '_', str($p.type_cond.param.element_identifier)) + "." + $p.type_cond.param.ext
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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25 #end if
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26 inputs/'$fname'
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27 #else
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28 '$p.type_cond.param'
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29 #end if
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30 #end for
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31 ]]></command>
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32 <configfiles>
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33 <configfile name="script">$code</configfile>
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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34 </configfiles>
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35 </xml>
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36 <xml name="inputs_macro">
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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37 <inputs>
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38 <repeat name="parameters" title="Parameters" min="1" default="1" help="Supply one or more parameters">
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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39 <conditional name="type_cond">
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40 <param name="type_sel" type="select" label="Parameter type">
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41 <option value="data">Dataset</option>
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42 <option value="text">Text</option>
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43 <!-- Not sure if int/float make sense .. can they be connected to text in WFs? -->
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44 </param>
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45 <when value="data">
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46 <param name="param" type="data" label="Dataset"/>
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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.">
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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48 <sanitizer invalid_char="_">
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49 <valid initial="string.ascii_letters,string.digits">
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50 <add value="_" />
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51 <add value="-" />
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52 <add value="." />
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53 </valid>
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54 </sanitizer>
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55 <!-- file names must not start with dash -->
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56 <validator type="regex" negate="true" message="Filenames must not start with a dash">^[-].*$</validator>
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57 </param>
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58 </when>
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59 <when value="text">
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60 <param name="param" type="text" label="Text parameter" help=""/>
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61 </when>
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62 </conditional>
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63 </repeat>
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64 <param name="code" type="text" area="true" label="@LANGUAGE@ program" help="">
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65 <sanitizer>
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66 <valid initial="string.printable"/>
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67 </sanitizer>
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68 </param>
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69 </inputs>
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70 </xml>
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71 <xml name="outputs_macro">
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72 <outputs>
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73 <collection name="output" type="list" label="Outputs">
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74 <discover_datasets pattern="__designation_and_ext__"/>
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75 </collection>
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76 </outputs>
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77 </xml>
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78
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79 <xml name="help_macro">
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80 <help><![CDATA[
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81 **Warning**
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82
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83 .. class:: warningmark
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84
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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85 **Make sure that you know what you are doing. When used wrong the tool may lead to
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86 data loss of files that you can write to.**
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87
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88 .. class:: warningmark
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89
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90 This tool is only intended to serve for single-use, ad-hoc exploratory analysis
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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91 of data sets with small @LANGUAGE@ scripts.
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92
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93 .. class:: warningmark
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94
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95 If you use this tool repeatedly with the same script and/or have the impression
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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96 that other Galaxy users could profit from this script then contact your local
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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97 Galaxy administrator or the Galaxy community, e.g. at https://github.com/galaxyproject/tools-iuc/,
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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98 and ask if your script can be turned into a proper Galaxy tool.
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99 One of the main advantages of a proper Galaxy tool is that they are tested and
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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100 maintained. Furthermore the whole Galaxy community may profit.
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101
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102 **What it does**
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103
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104 Executes an **@LANGUAGE@** script (in a @CONTAINER@ container).
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105
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106 An arbitrary number of data or text parameters can be given to the script.
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107 Data parameters are by default named like the datasets name and the datatype
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108 is used as extension. This can be overwritten with the filename parameter
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109 for the corresponding dataset.
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110
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111 @HELP_PARAMETERS@
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112
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113 @HELP_READ_FROM_STDIN@
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114
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115 Output datasets are read from the current working directory and put into a
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116 single collection. The collection elements will be named as the file names
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117 (without the extension). The file extension determines the datatype of the
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118 datasets (or Galaxy will try to autodetect the data type).
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119 ]]></help>
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120 </xml>
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121 </macros>