Mercurial > repos > iuc > raceid_trajectory

comparison macros.xml @ 4:3e5bb16abb55 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
author iuc
date Mon, 12 Aug 2019 13:02:23 -0400
parents ff7cd3c7c1df
children 72979cac22b2
comparison
equal deleted inserted replaced
3:da7ff78fe296 4:3e5bb16abb55
1 <macros> 1 <macros>
2 <token name="@GET_VERSION@"><![CDATA[ 2>&1 | head -1 | cut -d' ' -f 2 ]]></token>
3 <token name="@STRING2VECTOR@"> 2 <token name="@STRING2VECTOR@">
4 string2numericvector = function(string){ 3 string2numericvector = function(string){
5 #' Converts a string to a valid vector 4 #' Converts a string to a valid vector
6 #' 5 #'
7 #' e.g. "-1,2:5,2" evaluates to c(-1,2,3,4,5,2) 6 #' e.g. "-1,2:5,2" evaluates to c(-1,2,3,4,5,2)
25 #' e.g. "red,yellow,white" evaluates to c("red","yellow","white") 24 #' e.g. "red,yellow,white" evaluates to c("red","yellow","white")
26 return(unlist(strsplit(string,","))) 25 return(unlist(strsplit(string,",")))
27 } 26 }
28 </token> 27 </token>
29 <token name="@VERSION_RACEID@">3</token> 28 <token name="@VERSION_RACEID@">3</token>
30 <token name="@VERSION_PACKAGE@">0.2</token> 29 <token name="@VERSION_WRAPPER@">1</token>
30
31 <macro name="version_command_config" token_prog="temp" token_cheetah="temp2" token_out="2&#62; '$outlog'">
32 <version_command><![CDATA[
33 Rscript '$__tool_directory__/scripts/@PROG@' 2>&1 | head -1 | cut -d' ' -f 2
34 ]]></version_command>
35 <command detect_errors="exit_code"><![CDATA[
36 Rscript '$__tool_directory__/scripts/@PROG@' '$userconf' @OUT@
37 ]]>
38 </command>
39 <configfiles>
40 <configfile name="userconf" ><![CDATA[
41 @STRING2VECTOR@
42
43 @@CHEETAH@@
44 ]]></configfile>
45 </configfiles>
46 </macro>
47
31 <macro name="requirements" > 48 <macro name="requirements" >
32 <requirements> 49 <requirements>
33 <requirement type="package" version="0.1.1">r-raceid</requirement> 50 <requirement type="package" version="0.1.1">r-raceid</requirement>
34 <requirement type="package" version="1.6.2">bioconductor-scran</requirement> 51 <requirement type="package" version="1.6.2">bioconductor-scran</requirement>
35 </requirements> 52 </requirements>
66 <macro name="citations" > 83 <macro name="citations" >
67 <citations> 84 <citations>
68 <citation type="doi">10.1038/nature14966</citation> 85 <citation type="doi">10.1038/nature14966</citation>
69 <citation type="doi">10.1038/nmeth.4662</citation> 86 <citation type="doi">10.1038/nmeth.4662</citation>
70 </citations> 87 </citations>
71 </macro>
72 <macro name="select_cells" token_sectionname="@SECTIONNAME@" token_sectiontitle="@SECTIONTITLE@" >
73 <section name="@SECTIONNAME@" title="@SECTIONTITLE@" expanded="true" >
74 <param name="name_set" type="text" optional="true" label="Name of Set" >
75 <!-- Aname, Bname -->
76 <expand macro="sanitize_title" />
77 </param>
78 <conditional name="meth" >
79 <param name="type" type="select" label="Selection method" >
80 <option value="cln" selected="true">Cluster Numbers</option>
81 <option value="regex" >Regular Expression</option>
82 <option value="manual" >Manual Selection</option>
83 </param>
84 <when value="cln" >
85 <param name="selector" type="text" value="" label="List of clusters" >
86 <expand macro="sanitize_numeric_vector" />
87 </param>
88 </when>
89 <when value="regex" >
90 <param name="selector" type="text" value="" label="Regular Expression to select gene names" >
91 <expand macro="sanitize_regex" />
92 </param>
93 </when>
94 <when value="manual" >
95 <param name="selector" type="text" value="" label="List of genes" >
96 <expand macro="sanitize_string_vector" />
97 </param>
98 </when>
99 </conditional>
100 </section>
101 </macro> 88 </macro>
102 <!-- Sanitizers --> 89 <!-- Sanitizers -->
103 <macro name="sanitize_title"> 90 <macro name="sanitize_title">
104 <sanitizer invalid_char=""> 91 <sanitizer invalid_char="">
105 <valid initial="string.letters,string.digits" > 92 <valid initial="string.letters,string.digits" >