Mercurial > repos > iuc > raceid_filtnormconf

annotate macros.xml @ 0:8dc8ff057b0f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
author iuc
date Thu, 22 Nov 2018 04:44:44 -0500
parents
children 5d5b14dbd092
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8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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1 <macros>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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2 <token name="@GET_VERSION@"><![CDATA[ 2>&1 | head -1 | cut -d' ' -f 2 ]]></token>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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3 <token name="@STRING2VECTOR@">
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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4 string2numericvector = function(string){
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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5 #' Converts a string to a valid vector
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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6 #'
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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7 #' e.g. "-1,2:5,2" evaluates to c(-1,2,3,4,5,2)
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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8 #'
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9 #' @param add string2vector function to safe environment
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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10 #' @return vector of integers
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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11 terms = unlist(strsplit(string, split=","))
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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12 res = lapply(terms, function(x){
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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13 if (grepl(":",x)){
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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14 l_r = as.integer(c(unlist(strsplit(x,split=":"))))
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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15 return(seq(l_r[1],l_r[2]))
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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16 }
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17 return(as.integer(x))
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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18 })
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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19 return(c(unlist(res)))
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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20 }
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21
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22 string2textvector = function(string){
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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23 #' Converts a string to a valid string vector
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24 #'
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25 #' e.g. "red,yellow,white" evaluates to c("red","yellow","white")
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26 return(unlist(strsplit(string,",")))
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27 }
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28 </token>
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29 <token name="@VERSION_RACEID@">3</token>
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30 <token name="@VERSION_PACKAGE@">0.2</token>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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31 <macro name="requirements" >
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32 <requirements>
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33 <requirement type="package" version="0.1.1">r-raceid</requirement>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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34 <requirement type="package" version="1.6.2">bioconductor-scran</requirement>
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35 </requirements>
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36 </macro>
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37 <macro name="yesno_checkedno" >
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38 <option value="yes" >Yes</option>
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39 <option value="no" selected="true" >No</option>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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40 </macro>
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41 <macro name="use_defaults_no" >
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42 <conditional name="use" >
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43 <param name="def" type="select" label="Use Defaults?" >
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44 <option value="yes" selected="true" >Yes</option>
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45 <option value="no" >No</option>
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46 </param>
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47 <when value="yes" />
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48 <when value="no" >
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49 <yield />
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50 </when>
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51 </conditional>
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52 </macro>
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53 <macro name="test_nondef" >
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54 <conditional name="use" >
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55 <param name="def" value="no" />
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56 <yield />
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57 </conditional>
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58 </macro>
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59 <macro name="section_test_nondef" >
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60 <section name="@SECTIONNAME@" >
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61 <expand macro="test_nondef" >
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62 <yield />
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63 </expand>
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64 </section>
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65 </macro>
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66 <macro name="citations" >
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67 <citations>
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68 <citation type="doi">10.1038/nature14966</citation>
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69 <citation type="doi">10.1038/nmeth.4662</citation>
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70 </citations>
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71 </macro>
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72 <macro name="select_cells" token_sectionname="@SECTIONNAME@" token_sectiontitle="@SECTIONTITLE@" >
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73 <section name="@SECTIONNAME@" title="@SECTIONTITLE@" expanded="true" >
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74 <param name="name_set" type="text" optional="true" label="Name of Set" >
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75 <!-- Aname, Bname -->
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76 <expand macro="sanitize_title" />
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77 </param>
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78 <conditional name="meth" >
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79 <param name="type" type="select" label="Selection method" >
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80 <option value="cln" selected="true">Cluster Numbers</option>
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81 <option value="regex" >Regular Expression</option>
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82 <option value="manual" >Manual Selection</option>
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83 </param>
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84 <when value="cln" >
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85 <param name="selector" type="text" value="" label="List of clusters" >
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86 <expand macro="sanitize_numeric_vector" />
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87 </param>
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88 </when>
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89 <when value="regex" >
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90 <param name="selector" type="text" value="" label="Regular Expression to select gene names" >
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91 <expand macro="sanitize_regex" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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92 </param>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
93 </when>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
94 <when value="manual" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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95 <param name="selector" type="text" value="" label="List of genes" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
96 <expand macro="sanitize_string_vector" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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97 </param>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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98 </when>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
99 </conditional>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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diff changeset
100 </section>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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101 </macro>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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102 <!-- Sanitizers -->
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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103 <macro name="sanitize_title">
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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104 <sanitizer invalid_char="">
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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105 <valid initial="string.letters,string.digits" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
106 <add value=" " />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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107 <add value="_" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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108 </valid>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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109 </sanitizer>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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110 </macro>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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111 <macro name="sanitize_regex" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
112 <sanitizer invalid_char="">
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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diff changeset
113 <valid initial="string.letters,string.digits">
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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114 <add value="!"/>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
115 <add value="="/>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
116 <add value="-"/>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
117 <add value="."/>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
118 <add value="*"/>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
119 <add value="?"/>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
120 <add value="+"/>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
121 <add value="\\"/>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
122 <add value="_"/>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
123 <add value="|"/>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
124 <add value="&#91;"/> <!-- left square bracket, e.g subselecting from vec[1] -->
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
125 <add value="&#93;"/> <!-- right square bracket -->
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
126 <add value="&#40;"/> <!-- left parenthesis -->
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
127 <add value="&#41;"/> <!-- right parenthesis -->
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
128 </valid>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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diff changeset
129 </sanitizer>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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130 </macro>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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131 <macro name="sanitize_numeric_vector" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
132 <sanitizer invalid_char="">
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
133 <valid initial="string.digits">
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
134 <add value=","/>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
135 </valid>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
136 </sanitizer>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
137 </macro>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
138 <macro name="sanitize_string_vector" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
139 <sanitizer invalid_char="">
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
140 <valid initial="string.letters,string.digits">
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
141 <add value=","/>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
142 <add value="_"/>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
143 <add value="-"/>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
144 <add value="."/>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
145 </valid>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
146 </sanitizer>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
147 </macro>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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148 </macros>