toolfactory_gtn: toolfactory/rgToolFactory2.xml annotate

annotate toolfactory/rgToolFactory2.xml @ 3:c4f192ec521c draft

Uploaded

author	fubar
date	Tue, 20 Apr 2021 05:30:52 +0000
parents	b65ec4f387b9
children

rev	line source
0 43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	1 <tool id="rgtf2" name="toolfactory" version="2.00" profile="16.04" >
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	2 <description>Scripts into tools v2.0</description>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	3 <macros>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	4 <xml name="singleText">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	5 <param name="param_value" type="text" value="" label="Enter this parameter's default text value">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	6 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	7 </xml>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	8 <xml name="singleInt">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	9 <param name="param_value" type="integer" value="" label="Enter this parameter's default integer value" >
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	10 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	11 </xml>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	12 <xml name="singleFloat">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	13 <param name="param_value" type="float" value="" label="Enter this parameter's default value">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	14 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	15 </xml>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	16 <xml name="singleBoolean">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	17 <param name="param_value" type="boolean" value="" label="Enter this parameter's default value" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	18 <param name="truevalue" type="text" value="True" label="Command line value to emit when True" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	19 <param name="falsevalue" type="boolean" value="True" label="Command line value to emit when False" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	20 </xml>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	21 <xml name="selectText">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	22 <repeat name="selectTexts" title="Add each option to be presented in a text select box" min="2" default="2"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	23 help="Each text added here will also have a value to be emitted on the command line when the text is chosen">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	24 <param name="select_text" type="text" value="" label="Enter the explanatory text the user will see for this choice" >
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	25 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	26 <param name="select_value" type="text" value="" label="Enter the value for the command line when the user selects this option">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	27 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	28 </repeat>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	29 </xml>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	30 <xml name="tool_metadata">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	31 <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	32 help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	33 <param name="tool_desc" label="Tool Synopsis" type="text" value=""
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	34 help="Supply a brief tool description for the Galaxy tool menu entry" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	35 <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	36 value="What it Does"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	37 help="Supply user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" >
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	38 <sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	39 <valid initial="string.printable" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	40 <mapping initial="none"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	41 </sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	42 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	43 <repeat name="citations" title="Citation">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	44 <conditional name="citation_type">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	45 <param name="type" type="select" display="radio" label="Citation Type">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	46 <option value="doi">DOI</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	47 <option value="bibtex">BibTeX</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	48 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	49 <when value="doi">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	50 <param name="doi" label="DOI" type="text" value=""
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	51 help="Supply a DOI (e.g. doi: 10.1111/j.1740-9713.2007.00258.x) to be cited when this tool is used in published research." />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	52 </when>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	53 <when value="bibtex">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	54 <param name="bibtex" label="BibTex" type="text" area="true"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	55 help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" >
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	56 <sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	57 <valid initial="string.printable" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	58 <mapping initial="none"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	59 </sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	60 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	61 </when>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	62 </conditional>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	63 </repeat>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	64 </xml>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	65 <xml name="io">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	66 <section name="io" title="Input and output files" expanded="true">
3 c4f192ec521c Uploaded fubar parents: 2 diff changeset	67 <repeat name="history_inputs" title="Inputs" min="0"
c4f192ec521c Uploaded fubar parents: 2 diff changeset	68 help="Input data files to pass on the command line to the executable. USE SMALL SAMPLES for the new tool's test. Prompts will form a history item selector as input for users of this new tool">
0 43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	69 <param name="input_files" type="data" format="data" label="Select an input file from your history" multiple="false"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	70 help=""/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	71 <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	72 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	73 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	74 <column name="value" index="0"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	75 </options>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	76 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	77 <param name="input_label" type="text" value="" label="This will become the user prompt for the form so please make it informative" >
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	78 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	79 <param name="input_help" type="text" value="" label="This will become help text on the form." >
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	80 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	81 <param name="input_CL" type="text" label="Positional: ordinal integer. Argparse: argument name. STDIN if the executable/script expects it"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	82 help="If you will pass positional parameters, enter the integer ordinal for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value="">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	83 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	84 <param name="input_repeat" type="boolean" checked="False" truevalue="1" falsevalue="0" label="Allow user to repeat this input as many times as wanted - script/executable must parse these."/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	85 </repeat>
3 c4f192ec521c Uploaded fubar parents: 2 diff changeset	86 <repeat name="history_outputs" min="1" title="Outputs"
c4f192ec521c Uploaded fubar parents: 2 diff changeset	87 help="New history items output by the executable to appear in the user history after the tool runs. The name will become a history item for users of the new tool you are making containing one of it's outputs">
c4f192ec521c Uploaded fubar parents: 2 diff changeset	88 <param name="history_name" type="text" label="Output Name" optional="false"
c4f192ec521c Uploaded fubar parents: 2 diff changeset	89 help="Name used for this output in history. No spaces! Argparse will also use this name as --[name]">
0 43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	90 <sanitizer invalid_char="_">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	91 <valid initial="string.ascii_letters,string.digits" >
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	92 <add value="_" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	93 </valid>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	94 </sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	95 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	96 <param name="history_format" type="select" multiple="false" label="Select the datatype for this output"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	97 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	98 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	99 <column name="value" index="0"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	100 </options>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	101 </param>
3 c4f192ec521c Uploaded fubar parents: 2 diff changeset	102 <param name="history_CL" type="text" label="Position"
c4f192ec521c Uploaded fubar parents: 2 diff changeset	103 help="Positional: ordinal integer or 'STDOUT' if '>' required. Otherwise ignored if argparse because name is used. If positional parameters, enter the integer ordinal expected for this parameter. If argparse, ignore unless STDOUT needed" value=""/>
c4f192ec521c Uploaded fubar parents: 2 diff changeset	104 <param name="history_test" type="text" label="Output test criteria"
c4f192ec521c Uploaded fubar parents: 2 diff changeset	105 help="Pass/fail decision criterion for this output compared to test generation. Available options are diff:[lines], sim_size:[delta (integer) or delta_frac (float)" value="diff:0"/>
0 43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	106 </repeat>
3 c4f192ec521c Uploaded fubar parents: 2 diff changeset	107 <repeat name="collection_outputs" title="Output Collections" min="0"
c4f192ec521c Uploaded fubar parents: 2 diff changeset	108 help="New history collections to appear in the user history after the tool runs. Hides outputs not needed for downstream tools such as images and intermediate reports." default="0">
c4f192ec521c Uploaded fubar parents: 2 diff changeset	109 <param name="name" type="text" label="Name"
c4f192ec521c Uploaded fubar parents: 2 diff changeset	110 help="for new collection with all outputs not individually passed to history outputs. No spaces! Script MUST create and fill a directory with the same name and the tool test MUST be overwritten - see the plotter example for hints">
0 43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	111 <sanitizer invalid_char="_">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	112 <valid initial="string.ascii_letters,string.digits" >
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	113 <add value="_" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	114 </valid>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	115 </sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	116 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	117 <param name="kind" type="select" multiple="false" label="Select the kind of collection for this output"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	118 help="">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	119 <option value="list" selected="true">List</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	120 <option value="paired">Paired</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	121 <option value="list:paired">List of paired</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	122 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	123 <param name="label" type="text" label="Label for this collection" help="" value=""/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	124 <param name="discover" type="text" label="Discover datasets expression" help="__name_and_ext__ should catch all filenames with extensions" value="__name_and_ext__"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	125 </repeat>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	126
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	127 </section>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	128 </xml>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	129 <xml name="additparam">
3 c4f192ec521c Uploaded fubar parents: 2 diff changeset	130 <section name="addparam" title="Arguments" help="Executable or script settings passed on the command line other than I/O files" expanded="true">
0 43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	131 <param name="edit_params" type="select" display="radio" label="Make these settings on the generated tool form user editable?"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	132 help="If no, users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	133 <option value="yes" selected="true">Yes, allow user to edit all additional parameters on the generated tool form</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	134 <option value="no">No - use the fixed values for all additional parameters - no user editing</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	135 </param>
3 c4f192ec521c Uploaded fubar parents: 2 diff changeset	136 <repeat name="additional_parameters" title="Command Line Paramters" min="0"
c4f192ec521c Uploaded fubar parents: 2 diff changeset	137 help="Command line settings for the user to pass to the executable. See examples below to see how these can be parsed by scripts in the various languages">
0 43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	138 <param name="param_name" type="text" value="" label="Choose the name for this parameter - MUST not be blank!">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	139 <sanitizer invalid_char="">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	140 <valid initial="string.ascii_letters,string.digits"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	141 <mapping initial="none"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	142 </sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	143 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	144 <conditional name="ap_type">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	145 <param name="param_type" type="select" label="Select the type for this parameter">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	146 <option value="text" selected="true">Text string</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	147 <option value="integer">Integer</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	148 <option value="float">Float</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	149 <option value="boolean">Boolean</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	150 <option value="selecttext">Select text string</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	151 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	152 <when value = "text">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	153 <expand macro="singleText" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	154 </when>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	155 <when value = "integer">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	156 <expand macro="singleInt" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	157 </when>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	158 <when value = "float">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	159 <expand macro="singleFloat" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	160 </when>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	161 <when value = "boolean">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	162 <expand macro="singleBoolean" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	163 </when>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	164 <when value = "selecttext">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	165 <expand macro="selectText" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	166 </when>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	167 </conditional>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	168 <param name="param_label" type="text" value="" label="Enter this parameter's label for the form">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	169 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	170 <param name="param_help" type="text" value="" label="Help for this parameter">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	171 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	172 <param name="param_CL" type="text" label="Positional ordinal \| argparse argument name"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	173 help="Using positional parameters, enter the integer ordinal for this parameter on the command line. Using Argparse style, '--' will be prepended on the CL" value="" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	174 <param name="param_CLprefixed" type="text" label="Override the generated default argparse name prefix if not empty - eg ----foo if needed"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	175 help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root." value="" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	176 <param name="param_repeat" type="boolean" checked="False" truevalue="1" falsevalue="0" label="Allow user to repeat this as many times as needed." />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	177 </repeat>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	178 </section>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	179 </xml>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	180 </macros>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	181
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	182 <requirements>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	183 <requirement type="package" version="0.4.14">galaxyxml</requirement>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	184 <requirement type="package" version="0.74.3">planemo</requirement>
3 c4f192ec521c Uploaded fubar parents: 2 diff changeset	185 <requirement type="package" version="0.10.6">ephemeris</requirement>
0 43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	186 </requirements>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	187
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	188 <command detect_errors="exit_code"><![CDATA[
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	189 #import os
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	190 #set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1'
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	191 #if not $dev_env and ( $__user_email__ not in $__admin_users__ ):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	192 python3 $__tool_directory__/rgToolFactory2.py --bad_user $__user_email__
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	193 #else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	194 python3 $__tool_directory__/rgToolFactory2.py
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	195 #if len(str($cl_suffix)) > 0:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	196 --cl_suffix "$cl_suffix"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	197 #end if
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	198 #if $cover.commover == "yes":
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	199 #if len(str($cover.command_override)) > 10:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	200 --command_override "$commandoverride"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	201 #end if
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	202 #if len(str($cover.test_override)) > 10:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	203 --test_override "$testoverride"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	204 #end if
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	205 #end if
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	206 --packages "$deps.packages"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	207 #if $deps.usescript.choosescript == "yes":
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	208 --script_path "$runme"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	209 --sysexe "$deps.usescript.scriptrunner"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	210 #end if
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	211 --tool_name "$tool_name" --user_email "$__user_email__" --citations "$citeme" --parampass "$io_param.ppass.parampass"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	212
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	213 #if str($make.makeMode.make_Tool)!="runonly":
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	214 --make_Tool "$make.makeMode.make_Tool"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	215 --tool_desc "$make.makeMode.tool_desc"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	216 --tool_version "$make.makeMode.tool_version"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	217 --help_text "$helpme"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	218 --new_tool "$new_tool"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	219 --toolshed_api_key "$make.makeMode.toolshed_apikey"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	220 --galaxy_api_key "$make.makeMode.galaxy_apikey"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	221 --toolshed_url "$make.makeMode.toolshed_url"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	222 --galaxy_url "$make.makeMode.galaxy_url"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	223 #end if
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	224 #if $io_param.ppass.parampass != '0':
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	225 #if str($io_param.ppass.addparam.edit_params) == "yes":
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	226 --edit_additional_parameters
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	227 #end if
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	228 #for $apar in $io_param.ppass.addparam.additional_parameters:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	229 #if $apar.ap_type.param_type=="selecttext":
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	230 --selecttext_parameters '{"name":"$apar.param_name", "label":"$apar.param_label", "help":"$apar.param_help",
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	231 "type":"$apar.ap_type.param_type","CL":"$apar.param_CL","override":"$apar.param_CLprefixed","value": [
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	232 #for $i,$st in enumerate($apar.ap_type.selectTexts):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	233 "$st.select_value"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	234 #if ($i < (len($apar.ap_type.selectTexts)-1)):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	235 ,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	236 #end if
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	237 #end for
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	238 ], "texts": [
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	239 #for $i,$st in enumerate($apar.ap_type.selectTexts):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	240 "$st.select_text"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	241 #if ($i < (len($apar.ap_type.selectTexts)-1)):
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	242 ,
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	243 #end if
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	244
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	245 #end for
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	246 ]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	247 }'
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	248 #else:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	249 --additional_parameters '{"name": "$apar.param_name", "value": "$apar.ap_type.param_value", "label": "$apar.param_label", "help": "$apar.param_help",
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	250 "type": "$apar.ap_type.param_type","CL": "$apar.param_CL","override": "$apar.param_CLprefixed", "repeat": "$apar.param_repeat"}'
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	251 #end if
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	252 #end for
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	253 #end if
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	254 #for $intab in $io_param.ppass.io.history_inputs:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	255 --input_files '{"name": "$intab.input_files", "CL": "$intab.input_CL", "format": "$intab.input_formats", "label": "$intab.input_label", "help": "$intab.input_help", "repeat": "$intab.input_repeat"}'
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	256 #end for
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	257 #for $otab in $io_param.ppass.io.history_outputs:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	258 --output_files '{"name": "$otab.history_name", "format": "$otab.history_format", "CL": "$otab.history_CL", "test": "$otab.history_test"}'
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	259 #end for
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	260 #for $collect in $io_param.ppass.io.collection_outputs:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	261 --collection '{"name": "$collect.name", "kind": "$collect.kind", "discover": "$collect.discover", "label": "$collect.label"}'
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	262 #end for
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	263 --galaxy_root "$__root_dir__"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	264 --tool_dir "$__tool_directory__"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	265 #end if
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	266 ]]></command>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	267 <configfiles>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	268 <configfile name="runme">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	269 $deps.usescript.dynScript
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	270 </configfile>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	271 <configfile name="commandoverride">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	272 #if $cover.commover == "yes" and len(str($cover.command_override).strip()) > 1:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	273 $cover.command_override
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	274 #end if
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	275 </configfile>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	276 <configfile name="testoverride">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	277 #if $cover.commover == "yes" and len(str($cover.test_override).strip()) > 1:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	278 $cover.test_override
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	279 #end if
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	280 </configfile>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	281 <configfile name="helpme">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	282 #if $make.makeMode.make_Tool != "runonly":
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	283 ${make.makeMode.help_text}
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	284 #else
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	285 $tool_name help goes here
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	286 #end if
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	287 </configfile>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	288 <configfile name="citeme">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	289 #if $make.makeMode.make_Tool != "runonly":
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	290 #for $citation in $make.makeMode.citations:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	291 #if $citation.citation_type.type == "bibtex":
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	292 ENTRYbibtex
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	293 ${citation.citation_type.bibtex}
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	294 #else
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	295 ENTRYdoi
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	296 ${citation.citation_type.doi}
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	297 #end if
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	298 #end for
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	299 #end if
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	300 </configfile>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	301 </configfiles>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	302 <inputs>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	303 <param name="tool_name" type="text" value="tool1" label="New tool ID and title for outputs"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	304 help="Toolshed repository name. Choose thoughtfully to avoid namespace clashes with other tool writers. Lower case, digits and underscores only">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	305 <sanitizer invalid_char="">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	306 <valid initial="string.ascii_lowercase,string.digits">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	307 <add value="_"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	308 </valid>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	309 </sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	310 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	311
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	312 <section name="deps" title="Dependencies, optional script and script interpreter" expanded="true">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	313
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	314 <param name="packages" type="text" value="" label="Conda dependencies as package name[:version, name:version...]. These will always be available when this tool executes"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	315 help="Use =[ver] or :[ver] for specific version - 'bwa=0.17.0'. Default is latest. Will be used every time the tool is (re)run. Only Conda is currently supported" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	316
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	317 <conditional name="usescript">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	318 <param name="choosescript" type="select" display="radio" label="Supply a script for a dependency (e.g. python/R/bash) or a system executable such as Bash"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	319 help = "For script interpreters like Python or bash, parameters and i/o specified below must match script's expectations - if you pass parameters, the script must deal with them">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	320 <option value="no">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	321 <option value="yes" selected="true">Yes, a script is ready to be pasted below</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	322 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	323 <when value="no">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	324 <param name="dynScript" type="hidden" value="" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	325 <param name="scriptrunner" type="hidden" value="" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	326 </when>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	327 <when value="yes">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	328 <param name="scriptrunner" type="text" value="" label="Interpreter for the script - eg bash or python. Can be one of the dependencies named above or a system executable"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	329 help="Scripts are interpreted by the executable named here. For conda r-base, 'Rscript --vanilla' or for conda planemo, 'planemo test' for example">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	330 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	331 <param name="dynScript" type="text" area="True" value="" label="Script for executable above to interpret. It can be one of the Conda dependency names "
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	332 help="Script must handle all i/o and parameters as specified below using the parameters and passing method chosen below">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	333 <sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	334 <valid initial="string.printable"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	335 <mapping initial="none"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	336 </sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	337 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	338 </when>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	339 </conditional>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	340 </section>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	341 <section name="io_param" title="Data file input, output and settings forming the executable or script command line" expanded="true">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	342 <conditional name="ppass">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	343 <param name="parampass" type="select" display="radio" label="Command line parameter passing method to use">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	344 <option value="argparse" selected="true">Argparse: passed in the form of --clname value</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	345 <option value="positional">Positional: Passed in the order of positional ordinals ...foo.bam bar.idx zot.xls</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	346 <option value="0">Tool reads selected input file from STDIN and writes STDOUT with no parameters</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	347 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	348 <when value="argparse">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	349 <expand macro="io" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	350 <expand macro="additparam" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	351 </when>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	352 <when value="positional">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	353 <expand macro="io" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	354 <expand macro="additparam" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	355 </when>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	356 <when value="0">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	357 <expand macro="io"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	358 </when>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	359 </conditional>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	360 </section>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	361 <param name="cl_suffix" type="text" value="" label="Suffix for generated command line. Useful for bash post processing. Use override below to replace completely"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	362 help="';' separated bash commands can be used here for post processing - added at end of autogenerated command line">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	363 <sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	364 <valid initial="string.printable" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	365 <mapping initial="none"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	366 </sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	367 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	368 <conditional name="cover">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	369 <param name="commover" type="select" display="radio" label="Add Human wrought code to override the generated XML command and/or test section - DIY"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	370 help = "For arbitrary and artfull command lines. All i/o and parameters must be passed. Choose No unless needed. Not for the faint of heart">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	371 <option value="no" selected="true">No. Use automatically generated command/test XML </option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	372 <option value="yes">Yes. XML needed to override autogenerated command and/or test segments will be pasted below</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	373 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	374 <when value="no">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	375 <param name="command_override" type="hidden" value="" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	376 <param name="test_override" type="hidden" value="" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	377 </when>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	378 <when value="yes">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	379 <param name="command_override" type="text" area="True" value="" label="Optional. Human wrought command element override XML/template - e.g. for bwa"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	380 help="For arbitrary and artfull command lines. All i/o and parameters must be passed. Leave blank unless needed. Not for the faint of heart">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	381 <sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	382 <valid initial="string.printable"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	383 <mapping initial="none"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	384 </sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	385 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	386 <param name="test_override" type="text" area="True" value="" label="Optional. Human wrought test element override XML/template - e.g. for bwa"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	387 help="For arbitrary and artfull scripts. Leave blank unless needed. Not for the faint of heart">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	388 <sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	389 <valid initial="string.printable" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	390 <mapping initial="none"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	391 </sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	392 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	393 </when>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	394 </conditional>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	395 <section name="make" title="Generate, toolshed and local Galaxy installation options" expanded="true">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	396 <conditional name="makeMode">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	397 <param name="make_Tool" type="select" display="radio" label="Choose the steps you want to run. The TF Docker container is recommended for local installation"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	398 help="Installation in this Galaxy is optional" >
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	399 <option value="generate" >Run to generate tests only. Should fail if dependencies needed.</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	400 <option value="gentest" selected="true">Test with planemo after generating.</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	401 <option value="gentestinstall">Install in this Galaxy after generation and testing. Must have local ToolShed as in the TF Docker container</option>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	402 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	403 <when value="generate">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	404 <param name="galaxy_apikey" value="" type="hidden" ></param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	405 <param name="toolshed_apikey" value="" type="hidden" ></param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	406 <param name="galaxy_url" value="" type="hidden" ></param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	407 <param name="toolshed_url" value="" type="hidden" ></param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	408 <expand macro="tool_metadata" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	409 </when>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	410 <when value="gentest">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	411 <param name="galaxy_apikey" value="" type="hidden" ></param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	412 <param name="toolshed_apikey" value="" type="hidden" ></param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	413 <param name="galaxy_url" value="" type="hidden" ></param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	414 <param name="toolshed_url" value="" type="hidden" ></param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	415 <expand macro="tool_metadata" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	416 </when>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	417 <when value="gentestinstall">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	418 <param name="galaxy_url" type="text" value="http://localhost:8080" label="URL for the Galaxy server where the new tool should be installed"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	419 help="Default is localhost">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	420 <sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	421 <valid initial="string.printable" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	422 <mapping initial="none"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	423 </sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	424 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	425 <param name="galaxy_apikey" type="text" value="fakekey" label="API key for the Galaxy to install the new tool"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	426 help="Cut and paste from the admin user properties screen">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	427 <sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	428 <valid initial="string.ascii_letters,string.digits" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	429 <mapping initial="none"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	430 </sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	431 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	432 <param name="toolshed_url" type="text" value="http://localhost:9009" label="URL for the Toolshed where the new tool should be installed"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	433 help="Default value is localhost:9009">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	434 <sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	435 <valid initial="string.printable" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	436 <mapping initial="none"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	437 </sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	438 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	439 <param name="toolshed_apikey" type="text" value="fakekey" label="API key for the local toolshed to use when installing the tool"
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	440 help="Cut and paste from the admin user properties screen">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	441 <sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	442 <valid initial="string.ascii_letters,string.digits" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	443 <mapping initial="none"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	444 </sanitizer>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	445 </param>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	446 <expand macro="tool_metadata" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	447 </when>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	448 </conditional>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	449 </section>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	450 </inputs>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	451 <outputs>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	452
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	453 <data format="toolshed.gz" name="new_tool" label="${tool_name}_toolshed.gz" >
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	454 <filter>makeMode['make_Tool'] != "runonly"</filter>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	455 </data>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	456
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	457 <collection name="TF_run_report" type="list" label="${tool_name} outputs">
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	458 <discover_datasets pattern="__name_and_ext__" directory="TF_run_report_tempdir" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	459 </collection>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	460 </outputs>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	461 <tests>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	462 <test>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	463 <param name="user_email" value="admin@galaxy.org"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	464 <param name="input_files" value="input1_sample" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	465 <param name="input_CL" value="1" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	466 <param name="input_formats" value="txt" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	467 <param name="input_label" value="input" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	468 <param name="input_help" value="help" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	469 <param name="tool_name" value="pyrevpos" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	470 <param name="parampass" value="positional" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	471 <param name="make_Tool" value="gentest" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	472 <param name="tool_version" value="0.01" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	473 <param name="tool_desc" value="positional reverse" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	474 <param name="help_text" value="help text goes here" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	475 <param name="packages" value="python"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	476 <param name="history_name" value="output2" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	477 <param name="history_format" value="txt" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	478 <param name="history_CL" value="2" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	479 <param name="dynScript" value="import sys; inp = sys.argv[1]; outp = sys.argv[2]; inlist = open(inp,'r').readlines(); o = open(outp,'w'); rs = [''.join(list(reversed(x.rstrip()))) for x in inlist]; o.write('\n'.join(rs)); o.close()"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	480 <param name="choosescript" value="yes" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	481 <param name="script_path" value="$runme"/>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	482 <output name="new_tool" file="toolfactory_pyrevpos_tgz_sample" compare="sim_size" delta="6000" />
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	483 </test>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	484 </tests>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	485 <help>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	486
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	487 .. class:: warningmark
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	488
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	489 Details and attribution
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	490 (see GTF_)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	491
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	492 Local Admins ONLY
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	493 Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool.
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	494
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	495 If you find a bug
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	496 Please raise an issue, or even better, submit a pull request fixing it, on the github repository GTF_
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	497
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	498 What it does
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	499 This tool optionally generates normal workflow compatible first class Galaxy tools
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	500
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	501 Generated tools can run existing binary packages that become requirements, existing scripts, or new scripts pasted into this tool form.
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	502 Pasted scripts are written so they are part of the new tool and cannot be adjusted by the downstream user.
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	503 Binary packages are managed by the dependency subsystem - conda usually, so anything in bioconda or conda_forge is available for example.
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	504
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	505 Any number of parameters can be built into the new tool form for passing in to the script or executable at runtime.
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	506 These can be editable by the downstream user or baked in.
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	507
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	508 When you run this tool, your executable or script and supplied parameter values will be run to produce a canonical
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	509 set of outputs - these are used to construct a test for the new tool.
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	510
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	511 If tool generation is required, a new tarball compatible with any Galaxy toolshed is created.
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	512 It can be unpacked in your galaxy/tools directory and manually added to tool_conf.xml, or
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	513 installed into any toolshed from where it can be installed into your Galaxy.
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	514
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	515
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	516 .. class:: warningmark
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	517
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	518 Note to system administrators
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	519 This tool offers NO built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances.
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	520 Admin_users will have the power to do anything they want as the Galaxy user if you install this tool.
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	521
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	522 .. class:: warningmark
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	523
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	524 Use on public servers is STRONGLY discouraged for obvious reasons
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	525
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	526 The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always be checked carefully before installation.
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	527 We recommend that you follow the good code hygiene practices associated with safe toolshed practices.
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	528
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	529 Here's a sample python script that can be cut and pasted into the tool form, suitable for positional parameter passing:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	530
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	531 ::
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	532
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	533 # reverse order of text by row
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	534 import sys
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	535 inp = sys.argv[1]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	536 outp = sys.argv[2]
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	537 i = open(inp,'r').readlines()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	538 o = open(outp,'w')
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	539 for row in i:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	540 rs = row.rstrip()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	541 rs = list(rs)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	542 rs.reverse()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	543 o.write(''.join(rs))
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	544 o.write('\n')
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	545 o.close()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	546
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	547 With argparse style parameters:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	548
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	549 ::
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	550
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	551 # reverse order of text by row
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	552 import argparse
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	553 parser = argparse.ArgumentParser()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	554 a = parser.add_argument
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	555 a('--infile',default='')
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	556 a('--outfile',default=None)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	557 args = parser.parse_args()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	558 inp = args.infile
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	559 outp = args.outfile
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	560 i = open(inp,'r').readlines()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	561 o = open(outp,'w')
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	562 for row in i:
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	563 rs = row.rstrip()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	564 rs = list(rs)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	565 rs.reverse()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	566 o.write(''.join(rs))
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	567 o.write('\n')
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	568 o.close()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	569
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	570 R script to draw some plots - use a collection.
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	571
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	572 ::
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	573
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	574
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	575 \# note this script takes NO input because it generates random data
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	576 dir.create('plots')
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	577 for (i in 1:10) {
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	578 foo = runif(100)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	579 bar = rnorm(100)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	580 bar = foo + 0.05*bar
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	581 pdf(paste('plots/yet',i,"anotherplot.pdf",sep='_'))
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	582 plot(foo,bar,main=paste("Foo by Bar plot \#",i),col="maroon", pch=3,cex=0.6)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	583 dev.off()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	584 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	585 bar = as.matrix(foo)
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	586 pdf(paste('plots/yet',i,"anotherheatmap.pdf",sep='_'))
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	587 heatmap(bar,main='Random Heatmap')
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	588 dev.off()
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	589 }
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	590
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	591
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	592
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	593 Paper_
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	594
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	595 Licensing
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	596
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	597 Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	598 All rights reserved.
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	599 Licensed under the LGPL_
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	600
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	601 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	602 .. _GTF: https://github.com/fubar2/toolfactory
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	603 .. _Paper: https://academic.oup.com/bioinformatics/article/28/23/3139/192853
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	604
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	605
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	606 </help>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	607 <citations>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	608 <citation type="doi">10.1093/bioinformatics/bts573</citation>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	609 </citations>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	610 </tool>
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	611
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again fubar parents: diff changeset	612

Mercurial > repos > fubar > toolfactory_gtn

annotate toolfactory/rgToolFactory2.xml @ 3:c4f192ec521c draft