Mercurial > repos > mvdbeek > docker_scriptrunner

annotate scriptrunner.xml @ 11:8571d1c719ee draft

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planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ccb01d548a42beeacc01313218bff8c563da6fa9
author mvdbeek
date Sat, 09 Jul 2016 07:41:09 -0400
parents b6211faea403
children 81f85bafcc7c
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11
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1 <tool id="docker_scriptrunner" name="docker scriptrunner" version="0.1.6">
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2 <description>Runs scripts using docker</description>
0
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="0.4.0">docker-py</requirement>
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8 </requirements>
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9 <command>
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10 python "$__tool_directory__/scriptrunner.py"
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11 --script_path "$runme"
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12 --interpreter "$interpreter"
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13 --user_email "$__user_email__"
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14 #if $generate_simple_output.make_TAB=="yes":
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15 --output_tab "$tab_file"
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16 #end if
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17 #if $make_HTML.value=="yes":
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18 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
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19 #else:
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20 --output_dir "."
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21 #end if
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22 #if $additional_parameters != 'None':
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23 #for i in $additional_parameters:
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24 --additional_parameters
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25 "$i.param_name, $i.param_value"
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26 #end for
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27 #end if
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28 #if $input_files != 'None':
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29 --input_tab
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30 #for i in $input_files:
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31 $i.input
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32 #end for
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33 #for i in $input_files:
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34 --input_format
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35 #if str($i.in_format) == "None":
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36 "Any"
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37 #else
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38 "$i.in_format"
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39 #end if
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40 #end for
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41 #end if
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42 --docker_image "$docker_image"
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43 </command>
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44 <configfiles>
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45 <configfile name="runme">$dynScript</configfile>
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46 </configfiles>
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47 <inputs>
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48 <repeat name="input_files" title="Select input files">
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49 <param name="input" format="data" type="data" label="Select an input file from your history" optional="true" size="120"
0
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50 help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
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51 </repeat>
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52 <repeat name="additional_parameters" title="Set additional parameters">
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53 <param name="param_name" type="text" value="parameter_name" label="Choose a parameter name" size="20">
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54 <sanitizer invalid_char="">
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55 <valid initial="string.letters,string.digits"><add value="@_."/></valid>>
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56 </sanitizer>
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57 </param>
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58 <param name="param_value" type="text" value="parameter_value" label="Enter a parameter value" size="50">
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59 <sanitizer>
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60 <valid initial="string.printable">
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61 </valid>
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62 <mapping initial="none"/>
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63 </sanitizer>
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64 </param>
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65 </repeat>
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66 <param name="make_HTML" type="select" label="Create an HTML report with links to all output files and thumbnail links to PDF images" size="60"
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67 help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
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68 <option value="yes">Yes, arrange all outputs produced by my script as an HTML output</option>
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69 <option value="" selected="true">No, no HTML output file thanks</option>
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70 </param>
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71 <conditional name="generate_simple_output">
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72 <param name="make_TAB" type="select" label="Create a new history output alongside the HTML file specified above"
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73 help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes">
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74 <option value="yes" selected="true">My script writes to a new history output</option>
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75 <option value="">I do not want a new history output file</option>
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76 </param>
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77 <when value="yes">
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78 <param name="out_format" type="select" label="Select the datatype that your tool/script produces" help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml">
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79 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
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80 <column name="value" index="0"/>
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81 </options>
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82 </param>
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83 </when>
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84 <when value="">
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85 </when>
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86 </conditional>
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87 <param name="interpreter" type="select" label="Select the interpreter for your code">
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88 <option value="Rscript" selected="true">Rscript</option>
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89 <option value="python">python</option>
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90 <option value="perl">perl</option>
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91 <option value="sh">sh</option>
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92 </param>
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93 <param help="The script you are pasting will be run in this image. Make sure it contains the necessary tools" label="Select a docker image" name="docker_image" type="select">
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94 <options from_data_table="docker_scriptrunner_images"/>
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95 </param>
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96 <param name="dynScript" label="Copy and paste the script to be executed here" type="text" value="" area="True" size="8x120"
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97 help="Script must deal with two command line parameters: Path to input tabular file path (or 'None' if none selected) and path to output tabular history file (or 'None').">
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98 <sanitizer>
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99 <valid initial="string.printable">
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100 </valid>
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101 <mapping initial="none"/>
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102 </sanitizer>
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103 </param>
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104 </inputs>
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105 <outputs>
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106 <data format_source="input" name="tab_file">
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107 <filter>generate_simple_output['make_TAB'] == "yes"</filter>
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108 <actions>
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109 <action type="format">
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110 <option type="from_param" name="generate_simple_output.out_format" />
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111 </action>
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112 </actions>
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113 </data>
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114 <data format="html" name="html_file" >
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115 <filter>make_HTML == "yes"</filter>
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116 </data>
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117 </outputs>
11
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118 <tests>
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119 <test>
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120 <param name='input_tab' value='tf2_test_in.xls' ftype='tabular' />
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121 <param name="make_TAB" value="yes" />
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122 <param name="make_HTML" value="yes" />
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123 <param name="out_format" value="tabular" />
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124 <param name="interpreter" value='python' />
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125 <param name="runme" value="tf2_test_runme.py"/>
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126 <output name='output1' file='tf2_test_out.xls' compare='diff' lines_diff = '10'/>
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127 <output name='html_file' file="tf2_test.html" compare='diff' lines_diff = '10'/>
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128 </test>
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129 </tests>
0
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130 <expand macro="help_macro" />
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131 <expand macro="test_data_macro" />
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132 </tool>