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comparison FileMerger.xml @ 11:1dfc532aadd1 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 19:42:01 -0400
parents 7186f4354d84
children 8b871a67ba56
comparison
equal deleted inserted replaced
10:41d6ddc19497 11:1dfc532aadd1
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [File Handling]--> 3 <!--Proposed Tool Section: [File Handling]-->
4 <tool id="FileMerger" name="FileMerger" version="2.3.0"> 4 <tool id="FileMerger" name="FileMerger" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Merges several MS files into one file.</description> 5 <description>Merges several MS files into one file.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FileMerger</token> 7 <token name="@EXECUTABLE@">FileMerger</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[FileMerger 15 @EXT_FOO@
16 #import re
14 17
15 -in 18 ## Preprocessing
16 #for token in $param_in: 19 mkdir in &&
17 $token 20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
18 #end for 21 mkdir out &&
19 #if $param_out: 22 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
20 -out $param_out 23 mkdir rt_concat_trafo_out &&
21 #end if
22 #if $param_annotate_file_origin:
23 -annotate_file_origin
24 #end if
25 #if $param_rt_concat_gap:
26 -rt_concat:gap $param_rt_concat_gap
27 #end if 24 #end if
28 25
29 #if $rep_param_rt_concat_trafo_out: 26 ## Main program call
30 -rt_concat:trafo_out 27
31 #for token in $rep_param_rt_concat_trafo_out: 28 set -o pipefail &&
32 #if " " in str(token): 29 @EXECUTABLE@ -write_ctd ./ &&
33 "$token.param_rt_concat_trafo_out" 30 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
34 #else 31 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
35 $token.param_rt_concat_trafo_out 32 -in
36 #end if 33 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
37 #end for 34 -out
35 'out/output.${out_type}'
36 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
37 -rt_concat:trafo_out
38 ${' '.join(["'rt_concat_trafo_out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])}
38 #end if 39 #end if
39 #if $param_raw_rt_auto: 40 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
40 -raw:rt_auto 41 | tee '$stdout'
41 #end if 42 #end if
42 43
43 #if $rep_param_raw_rt_custom: 44 ## Postprocessing
44 -raw:rt_custom 45 && mv 'out/output.${out_type}' '$out'
45 #for token in $rep_param_raw_rt_custom: 46 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
46 #if " " in str(token): 47 ${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'rt_concat_trafo_out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("trafoxml")} for _ in $rt_concat_trafo_out if _])}
47 "$token.param_raw_rt_custom"
48 #else
49 $token.param_raw_rt_custom
50 #end if
51 #end for
52 #end if 48 #end if
53 #if $param_raw_rt_filename: 49 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
54 -raw:rt_filename 50 && mv '@EXECUTABLE@.ctd' '$ctd_out'
55 #end if 51 #end if]]></command>
56 #if $param_raw_ms_level: 52 <configfiles>
57 -raw:ms_level $param_raw_ms_level 53 <inputs name="args_json" data_style="paths"/>
58 #end if 54 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
59 #if $adv_opts.adv_opts_selector=='advanced': 55 </configfiles>
60 #if $adv_opts.param_force:
61 -force
62 #end if
63 #end if
64 ]]></command>
65 <inputs> 56 <inputs>
66 <param name="param_in" type="data" format="mzData,mzxml,mzml,dta,dta2d,mgf,featurexml,consensusxml,fid,traml,fasta" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) "> 57 <param name="in" argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml" multiple="true" optional="false" label="Input files separated by blank" help=" select consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml data sets(s)"/>
67 <sanitizer> 58 <param name="out_type" type="select" optional="false" label="File type of output out (Output file)">
68 <valid initial="string.printable"> 59 <option value="mzML">mzml</option>
69 <remove value="'"/> 60 <option value="featureXML">featurexml</option>
70 <remove value="&quot;"/> 61 <option value="consensusXML">consensusxml</option>
71 </valid> 62 <option value="traML">traml</option>
72 </sanitizer> 63 <option value="fasta">fasta</option>
73 </param> 64 </param>
74 <param name="param_annotate_file_origin" display="radio" type="boolean" truevalue="-annotate_file_origin" falsevalue="" checked="false" optional="True" label="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)" help="(-annotate_file_origin) "/> 65 <param name="annotate_file_origin" argument="-annotate_file_origin" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)" help=""/>
75 <param name="param_rt_concat_gap" type="float" value="0.0" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" help="(-gap) RT concatenation is enabled if a value &gt; 0 is set"/> 66 <param name="append_method" argument="-append_method" display="radio" type="select" optional="false" label="Append consensusMaps rowise or colwise" help="(Please use colwise for the MSstatsConverter)">
76 <param name="param_raw_rt_auto" display="radio" type="boolean" truevalue="-raw:rt_auto" falsevalue="" checked="false" optional="True" label="Assign retention times automatically (integers starting at 1)" help="(-rt_auto) "/> 67 <option value="append_rows" selected="true">append_rows</option>
77 <repeat name="rep_param_raw_rt_custom" min="0" title="param_raw_rt_custom"> 68 <option value="append_cols">append_cols</option>
78 <param name="param_raw_rt_custom" type="text" size="30" value="0" label="List of custom retention times that are assigned to the files" help="(-rt_custom) The number of given retention times must be equal to the number of input files"> 69 <expand macro="list_string_san"/>
79 <sanitizer> 70 </param>
80 <valid initial="string.printable"> 71 <section name="rt_concat" title="Options for concatenating files in the retention time (RT) dimension" help="The RT ranges of inputs are adjusted so they don't overlap in the merged file (traML input not supported)" expanded="false">
81 <remove value="'"/> 72 <param name="gap" argument="-rt_concat:gap" type="float" optional="true" value="0.0" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" help="RT concatenation is enabled if a value &gt; 0 is set"/>
82 <remove value="&quot;"/> 73 </section>
83 </valid> 74 <section name="raw" title="Options for raw data input/output (primarily for DTA files)" help="" expanded="false">
84 </sanitizer> 75 <param name="rt_auto" argument="-raw:rt_auto" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assign retention times automatically (integers starting at 1)" help=""/>
76 <param name="rt_custom" argument="-raw:rt_custom" type="text" optional="true" value="" label="List of custom retention times that are assigned to the files" help="The number of given retention times must be equal to the number of input files (space separated list, in order to allow for spaces in list items surround them by single quotes)">
77 <expand macro="list_float_valsan"/>
85 </param> 78 </param>
86 </repeat> 79 <param name="rt_filename" argument="-raw:rt_filename" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to guess the retention time of a file based on the filename" help="This option is useful for merging DTA files, where filenames should contain the string 'rt' directly followed by a floating point number, e.g. 'my_spectrum_rt2795.15.dta'"/>
87 <param name="param_raw_rt_filename" display="radio" type="boolean" truevalue="-raw:rt_filename" falsevalue="" checked="false" optional="True" label="Try to guess the retention time of a file based on the filename. This option is useful for merging DTA files, where filenames should contain the string 'rt' directly followed by a floating point number," help="(-rt_filename) e.g. 'my_spectrum_rt2795.15.dta'"/> 80 <param name="ms_level" argument="-raw:ms_level" type="integer" optional="true" value="0" label="If 1 or higher, this number is assigned to spectra as the MS level" help="This option is useful for DTA files which do not contain MS level information"/>
88 <param name="param_raw_ms_level" type="integer" value="0" label="If 1 or higher, this number is assigned to spectra as the MS level" help="(-ms_level) This option is useful for DTA files which do not contain MS level information"/> 81 </section>
89 <expand macro="advanced_options"> 82 <expand macro="adv_opts_macro">
90 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 83 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
84 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
85 <expand macro="list_string_san"/>
86 </param>
91 </expand> 87 </expand>
88 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
89 <option value="trafo_out_FLAG">trafo_out (If 1 or higher, this number is assigned to spectra as the MS level)</option>
90 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
91 </param>
92 </inputs> 92 </inputs>
93 <outputs> 93 <outputs>
94 <data name="param_out" format="featurexml"/> 94 <data name="out" label="${tool.name} on ${on_string}: out">
95 <data name="param_rt_concat_trafo_out" format="trafoxml"/> 95 <change_format>
96 <when input="out_type" value="consensusXML" format="consensusxml"/>
97 <when input="out_type" value="fasta" format="fasta"/>
98 <when input="out_type" value="featureXML" format="featurexml"/>
99 <when input="out_type" value="mzML" format="mzml"/>
100 <when input="out_type" value="traML" format="traml"/>
101 </change_format>
102 </data>
103 <collection type="list" name="rt_concat_trafo_out" label="${tool.name} on ${on_string}: rt_concat:trafo_out">
104 <discover_datasets directory="rt_concat.trafo_out" format="trafoxml" pattern="__name__"/>
105 <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
106 </collection>
107 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
108 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
109 </data>
96 </outputs> 110 </outputs>
97 <help>Merges several MS files into one file. 111 <tests>
112 <expand macro="autotest_FileMerger"/>
113 <expand macro="manutest_FileMerger"/>
114 </tests>
115 <help><![CDATA[Merges several MS files into one file.
98 116
99 117
100 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FileMerger.html</help> 118 For more information, visit http://www.openms.de/documentation/TOPP_FileMerger.html]]></help>
119 <expand macro="references"/>
101 </tool> 120 </tool>