Mercurial > repos > iuc > raceid_inspectclusters

annotate macros.xml @ 7:be4646256624 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit b461ba94158cf4cc793919470b78bd3eb91312eb"
author iuc
date Thu, 02 Dec 2021 16:22:55 +0000
parents 41f34e925bd5
children 2b0d3e2f402a
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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>
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28 <token name="@TOOL_VERSION@">0.2.3</token>
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29 <token name="@VERSION_SUFFIX@">1</token>
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30
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31 <macro name="version_command_config" token_prog="temp" token_cheetah="temp2" token_out="2&#62; '$outlog'">
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32 <version_command><![CDATA[
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33 Rscript '$__tool_directory__/scripts/@PROG@' 2>&1 | head -1 | cut -d' ' -f 2
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34 ]]></version_command>
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35 <command detect_errors="exit_code"><![CDATA[
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36 Rscript '$__tool_directory__/scripts/@PROG@' '$userconf' @OUT@
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37 ]]>
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38 </command>
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39 <configfiles>
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40 <configfile name="userconf" ><![CDATA[
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41 @STRING2VECTOR@
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42
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43 @@CHEETAH@@
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44 ]]></configfile>
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45 </configfiles>
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46 </macro>
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47
0
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48 <macro name="requirements" >
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49 <requirements>
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50 <requirement type="package" version="@TOOL_VERSION@" >r-raceid</requirement>
6
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51 <!-- <requirement type="package" version="1.6.2">bioconductor-scran</requirement> -->
0
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52 </requirements>
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53 </macro>
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54 <macro name="yesno_checkedno" >
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55 <option value="yes" >Yes</option>
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56 <option value="no" selected="true" >No</option>
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57 </macro>
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58 <macro name="use_defaults_no" >
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59 <conditional name="use" >
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60 <param name="def" type="select" label="Use Defaults?" >
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61 <option value="yes" selected="true" >Yes</option>
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62 <option value="no" >No</option>
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63 </param>
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64 <when value="yes" />
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65 <when value="no" >
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66 <yield />
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67 </when>
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68 </conditional>
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69 </macro>
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70 <macro name="test_nondef" >
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71 <conditional name="use" >
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72 <param name="def" value="no" />
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73 <yield />
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74 </conditional>
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75 </macro>
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76 <macro name="section_test_nondef" >
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77 <section name="@SECTIONNAME@" >
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78 <expand macro="test_nondef" >
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79 <yield />
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80 </expand>
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81 </section>
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82 </macro>
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83 <macro name="citations" >
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84 <citations>
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85 <citation type="doi">10.1038/nature14966</citation>
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86 <citation type="doi">10.1038/nmeth.4662</citation>
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87 </citations>
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88 </macro>
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89 <!-- Sanitizers -->
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90 <macro name="sanitize_title">
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
91 <sanitizer invalid_char="">
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
92 <valid initial="string.letters,string.digits" >
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
93 <add value=" " />
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
94 <add value="_" />
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
95 </valid>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
96 </sanitizer>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
97 </macro>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
98 <macro name="sanitize_regex" >
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
99 <sanitizer invalid_char="">
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
100 <valid initial="string.letters,string.digits">
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
101 <add value="!"/>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
102 <add value="="/>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
103 <add value="-"/>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
104 <add value="."/>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
105 <add value="*"/>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
106 <add value="?"/>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
107 <add value="+"/>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
108 <add value="\\"/>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
109 <add value="_"/>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
110 <add value="|"/>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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111 <add value="&#91;"/> <!-- left square bracket, e.g subselecting from vec[1] -->
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
112 <add value="&#93;"/> <!-- right square bracket -->
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
113 <add value="&#40;"/> <!-- left parenthesis -->
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
114 <add value="&#41;"/> <!-- right parenthesis -->
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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115 </valid>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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116 </sanitizer>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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117 </macro>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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118 <macro name="sanitize_numeric_vector" >
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
119 <sanitizer invalid_char="">
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
120 <valid initial="string.digits">
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
121 <add value=","/>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
122 </valid>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
123 </sanitizer>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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124 </macro>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
125 <macro name="sanitize_string_vector" >
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
126 <sanitizer invalid_char="">
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
127 <valid initial="string.letters,string.digits">
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
128 <add value=","/>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
129 <add value="_"/>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
130 <add value="-"/>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
131 <add value="."/>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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132 </valid>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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133 </sanitizer>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
134 </macro>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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135 </macros>