openms_idmassaccuracy: macros.xml annotate

annotate macros.xml @ 17:14955951902f draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"

author	galaxyp
date	Sun, 13 Dec 2020 15:26:17 +0000
parents	e429563831f6
children

rev	line source
0 fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	1 <?xml version='1.0' encoding='UTF-8'?>
13 a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	2 <!-- CTD2Galaxy depends on this file and on the stdio, advanced_options macros!
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	3 You can edit this file to add your own macros, if you so desire, or you can
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	4 add additional macro files using the m/macros parameter -->
0 fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	5 <macros>
15 a1d4567a546e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	6 <token name="@TOOL_VERSION@">2.6</token>
13 a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	7 <token name="@GALAXY_VERSION@">0</token>
0 fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	8 <xml name="requirements">
fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	9 <requirements>
13 a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	10 <requirement type="package" version="@TOOL_VERSION@">openms</requirement>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	11 <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	12 <!-- makeblastdb for OMSSAAdapter -->
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	13 <requirement type="package" version="2.9.0">blast</requirement>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	14 <!--<requirement type="package" version="5.0.0">tpp</requirement>-->
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	15 <!-- for realpath (used e.g. in LuciphorAdapter) -->
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	16 <!--<requirement type="package" version="8.25">coreutils</requirement>-->
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	17 <requirement type="package" version="1.4">ctdopts</requirement>
6 aa6c9eec2297 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d2b76821e22b13ed6e21795ac1b82446d8f594c6 galaxyp parents: 3 diff changeset	18 <yield/>
0 fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	19 </requirements>
fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	20 </xml>
fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	21 <xml name="stdio">
fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	22 <stdio>
16 e429563831f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 2adf8edc3de4e1cd3b299b26abb14544d17d0636" galaxyp parents: 15 diff changeset	23 <regex match="std::bad_alloc" level="fatal_oom" description="Could not allocate memory"/>
17 14955951902f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty" galaxyp parents: 16 diff changeset	24 <regex match="OutOfMemoryError" level="fatal_oom" description="Could not allocate memory"/>
12 5c0d8041744c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5 galaxyp parents: 6 diff changeset	25 <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/>
5c0d8041744c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5 galaxyp parents: 6 diff changeset	26 <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/>
5c0d8041744c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5 galaxyp parents: 6 diff changeset	27 <regex match="qUncompress: could not allocate enough memory to uncompress data" level="fatal_oom" description="Java memory Exception"/>
0 fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	28 </stdio>
fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	29 </xml>
fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	30 <xml name="references">
fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	31 <citations>
fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	32 <citation type="doi">doi:10.1186/1471-2105-9-163</citation>
fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	33 </citations>
fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	34 </xml>
13 a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	35 <xml name="adv_opts_macro">
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	36 <conditional name="adv_opts_cond">
0 fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	37 <param name="adv_opts_selector" type="select" label="Advanced Options">
fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	38 <option value="basic" selected="True">Hide Advanced Options</option>
fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	39 <option value="advanced">Show Advanced Options</option>
fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	40 </param>
fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	41 <when value="basic"/>
fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	42 <when value="advanced">
fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	43 <yield/>
fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	44 </when>
fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	45 </conditional>
fc8ae76781bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	46 </xml>
13 a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	47
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	48 <!-- sanitizers and validators -->
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	49 <xml name="list_string_val">
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	50 <validator type="regex" message="parameter must not start with $">^[^$]</validator>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	51
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	52 <validator type="regex" message="a space separated list of string is needed (strings that contain spaces can be quoted with ")">^ ((?:\"[^\"]\" +)\|(?:[^ \"]+ +))((?:\"[^\"]\")\|(?:[^ \"]+)) *$</validator>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	53 </xml>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	54 <xml name="list_string_san">
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	55 <sanitizer>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	56 <valid initial="string.printable">
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	57 <!-- <remove value="'"/>-->
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	58 <!-- <remove value="\"/>--><!-- otherwise the user could quote the final quote -->
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	59 <!-- <remove value="`"/>-->
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	60 <!-- <remove value="$"/>-->
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	61 <!-- <remove value="<"/>-->
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	62 <!--<remove value="&"/> removed for MascotAdapterOnline -Mascot_server:export_params which is a URL POST string which can contain & .. could be mapped to & but there is still a & -->
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	63 <!--<remove value=";"/>-->
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	64 <!-- <remove value="#"/>-->
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	65 </valid>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	66 </sanitizer>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	67 </xml>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	68 <xml name="list_float_valsan">
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	69 <validator type="regex" message="a space separated list of float values is required">^ [-+]?[0-9]\.?[0-9]+([eE][-+]?[0-9]+)?( [-+]?[0-9]\.?[0-9]+([eE][-+]?[0-9]+)?)* *$</validator>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	70 <yield/>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	71 <sanitizer>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	72 <valid initial="string.digits">
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	73 <add value=" "/>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	74 <add value="."/>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	75 <add value="E"/>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	76 <add value="e"/>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	77 <add value="+"/>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	78 <add value="-"/>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	79 </valid>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	80 </sanitizer>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	81 </xml>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	82 <xml name="list_integer_valsan">
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	83 <validator type="regex" message="a space separated list of integer values is required">^ [+-]?[0-9]+( [+-]?[0-9]+)* *$</validator>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	84 <yield/>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	85 <sanitizer>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	86 <valid initial="string.digits">
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	87 <add value=" "/>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	88 <add value="+"/>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	89 <add value="-"/>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	90 </valid>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	91 </sanitizer>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	92 </xml>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	93
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	94 <!-- helper function to quote space separated strings -->
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	95 <token name="@QUOTE_FOO@">
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	96 #def quote(s):
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	97 #set $s = [ _ for _ in $s.split(" ") if _ != "" ]
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	98 #set $q = False
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	99 #for $i, $p in enumerate($s):
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	100 #if $p == "":
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	101 #continue
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	102 #end if
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	103 #if $p.startswith('"'):
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	104 #set $q = True
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	105 #end if
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	106 ## #if p.startswith('-'):
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	107 ## #set p = "\\" + p
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	108 ## #elif p.startswith('"-'):
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	109 ## #set p = "\\" + p[1:]
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	110 ## #end if
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	111 #if not $q:
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	112 #set $s[i] = '"%s"' % p
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	113 #end if
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	114 #if $p.endswith('"'):
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	115 #set $q = False
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	116 #end if
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	117 #end for
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	118 #return " ".join($s)
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	119 #end def
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	120 </token>
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	121
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	122 <token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o)
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	123 #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'}
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	124 #return m[o]
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	125 #end def
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	126 #def gxy2omsext(g)
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	127 #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'}
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	128 #return m[g]
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	129 #end def
a6da1e548e9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	130 ]]></token></macros>

Mercurial > repos > galaxyp > openms_idmassaccuracy

annotate macros.xml @ 17:14955951902f draft default tip