Mercurial > repos > iuc > raceid_clustering

annotate macros.xml @ 9:0bff0ee0683a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf
author iuc
date Wed, 24 Aug 2022 18:09:06 +0000
parents f911a64454fb
children
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1 <macros>
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2 <token name="@STRING2VECTOR@">
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3 string2numericvector = function(string){
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4 #' Converts a string to a valid vector
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5 #'
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6 #' e.g. "-1,2:5,2" evaluates to c(-1,2,3,4,5,2)
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7 #'
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8 #' @param add string2vector function to safe environment
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9 #' @return vector of integers
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10 terms = unlist(strsplit(string, split=","))
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11 res = lapply(terms, function(x){
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12 if (grepl(":",x)){
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13 l_r = as.integer(c(unlist(strsplit(x,split=":"))))
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14 return(seq(l_r[1],l_r[2]))
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15 }
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16 return(as.integer(x))
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17 })
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18 return(c(unlist(res)))
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19 }
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20
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21 string2textvector = function(string){
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22 #' Converts a string to a valid string vector
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23 #'
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24 #' e.g. "red,yellow,white" evaluates to c("red","yellow","white")
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25 return(unlist(strsplit(string,",")))
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26 }
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27 </token>
7
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28 <token name="@TOOL_VERSION@">0.2.3</token>
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29 <token name="@VERSION_SUFFIX@">3</token>
8
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30 <token name="@PROFILE@">21.01</token>
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31
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32 <macro name="version_command_config" token_prog="temp" token_cheetah="temp2" token_out="2&#62; '$outlog'">
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33 <version_command><![CDATA[
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34 Rscript '$__tool_directory__/scripts/@PROG@' 2>&1 | head -1 | cut -d' ' -f 2
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35 ]]></version_command>
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36 <command detect_errors="exit_code"><![CDATA[
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37 Rscript '$__tool_directory__/scripts/@PROG@' '$userconf' @OUT@
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38 ]]>
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39 </command>
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40 <configfiles>
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41 <configfile name="userconf" ><![CDATA[
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42 @STRING2VECTOR@
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43
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44 @@CHEETAH@@
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45 ]]></configfile>
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46 </configfiles>
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47 </macro>
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48
0
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49 <macro name="requirements" >
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50 <requirements>
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51 <requirement type="package" version="@TOOL_VERSION@" >r-raceid</requirement>
6
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52 <!-- <requirement type="package" version="1.6.2">bioconductor-scran</requirement> -->
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53 </requirements>
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54 </macro>
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55 <macro name="yesno_checkedno" >
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56 <option value="yes" >Yes</option>
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57 <option value="no" selected="true" >No</option>
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58 </macro>
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59 <macro name="use_defaults_no" >
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60 <conditional name="use" >
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61 <param name="def" type="select" label="Use Defaults?" >
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62 <option value="yes" selected="true" >Yes</option>
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63 <option value="no" >No</option>
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64 </param>
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65 <when value="yes" />
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66 <when value="no" >
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67 <yield />
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68 </when>
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69 </conditional>
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70 </macro>
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71 <macro name="test_nondef" >
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72 <conditional name="use" >
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73 <param name="def" value="no" />
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74 <yield />
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75 </conditional>
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76 </macro>
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77 <macro name="section_test_nondef" >
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78 <section name="@SECTIONNAME@" >
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79 <expand macro="test_nondef" >
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80 <yield />
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81 </expand>
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82 </section>
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83 </macro>
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84 <macro name="citations" >
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85 <citations>
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86 <citation type="doi">10.1038/nature14966</citation>
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87 <citation type="doi">10.1038/nmeth.4662</citation>
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88 </citations>
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89 </macro>
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90 <!-- Sanitizers -->
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91 <macro name="sanitize_title">
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92 <sanitizer invalid_char="">
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
93 <valid initial="string.letters,string.digits" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
94 <add value=" " />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
95 <add value="_" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
96 </valid>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
97 </sanitizer>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
98 </macro>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
99 <macro name="sanitize_regex" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
100 <sanitizer invalid_char="">
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
101 <valid initial="string.letters,string.digits">
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
102 <add value="!"/>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
103 <add value="="/>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
104 <add value="-"/>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
105 <add value="."/>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
106 <add value="*"/>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
107 <add value="?"/>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
108 <add value="+"/>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
109 <add value="\\"/>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
110 <add value="_"/>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
111 <add value="|"/>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
112 <add value="&#91;"/> <!-- left square bracket, e.g subselecting from vec[1] -->
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
113 <add value="&#93;"/> <!-- right square bracket -->
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
114 <add value="&#40;"/> <!-- left parenthesis -->
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
115 <add value="&#41;"/> <!-- right parenthesis -->
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
116 </valid>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
117 </sanitizer>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
118 </macro>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
119 <macro name="sanitize_numeric_vector" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
120 <sanitizer invalid_char="">
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
121 <valid initial="string.digits">
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
122 <add value=","/>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
123 </valid>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
124 </sanitizer>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
125 </macro>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
126 <macro name="sanitize_string_vector" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
127 <sanitizer invalid_char="">
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
128 <valid initial="string.letters,string.digits">
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
129 <add value=","/>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
130 <add value="_"/>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
131 <add value="-"/>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
132 <add value="."/>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
133 </valid>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
134 </sanitizer>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
135 </macro>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
136 </macros>