Mercurial > repos > iuc > raceid_trajectory
view macros.xml @ 1:30d9118a650a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 71e6b205841c83391ea8fc69e10eac03f212f4d6
author | iuc |
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date | Thu, 28 Feb 2019 12:59:30 -0500 |
parents | ff7cd3c7c1df |
children | 3e5bb16abb55 |
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<macros> <token name="@GET_VERSION@"><![CDATA[ 2>&1 | head -1 | cut -d' ' -f 2 ]]></token> <token name="@STRING2VECTOR@"> string2numericvector = function(string){ #' Converts a string to a valid vector #' #' e.g. "-1,2:5,2" evaluates to c(-1,2,3,4,5,2) #' #' @param add string2vector function to safe environment #' @return vector of integers terms = unlist(strsplit(string, split=",")) res = lapply(terms, function(x){ if (grepl(":",x)){ l_r = as.integer(c(unlist(strsplit(x,split=":")))) return(seq(l_r[1],l_r[2])) } return(as.integer(x)) }) return(c(unlist(res))) } string2textvector = function(string){ #' Converts a string to a valid string vector #' #' e.g. "red,yellow,white" evaluates to c("red","yellow","white") return(unlist(strsplit(string,","))) } </token> <token name="@VERSION_RACEID@">3</token> <token name="@VERSION_PACKAGE@">0.2</token> <macro name="requirements" > <requirements> <requirement type="package" version="0.1.1">r-raceid</requirement> <requirement type="package" version="1.6.2">bioconductor-scran</requirement> </requirements> </macro> <macro name="yesno_checkedno" > <option value="yes" >Yes</option> <option value="no" selected="true" >No</option> </macro> <macro name="use_defaults_no" > <conditional name="use" > <param name="def" type="select" label="Use Defaults?" > <option value="yes" selected="true" >Yes</option> <option value="no" >No</option> </param> <when value="yes" /> <when value="no" > <yield /> </when> </conditional> </macro> <macro name="test_nondef" > <conditional name="use" > <param name="def" value="no" /> <yield /> </conditional> </macro> <macro name="section_test_nondef" > <section name="@SECTIONNAME@" > <expand macro="test_nondef" > <yield /> </expand> </section> </macro> <macro name="citations" > <citations> <citation type="doi">10.1038/nature14966</citation> <citation type="doi">10.1038/nmeth.4662</citation> </citations> </macro> <macro name="select_cells" token_sectionname="@SECTIONNAME@" token_sectiontitle="@SECTIONTITLE@" > <section name="@SECTIONNAME@" title="@SECTIONTITLE@" expanded="true" > <param name="name_set" type="text" optional="true" label="Name of Set" > <!-- Aname, Bname --> <expand macro="sanitize_title" /> </param> <conditional name="meth" > <param name="type" type="select" label="Selection method" > <option value="cln" selected="true">Cluster Numbers</option> <option value="regex" >Regular Expression</option> <option value="manual" >Manual Selection</option> </param> <when value="cln" > <param name="selector" type="text" value="" label="List of clusters" > <expand macro="sanitize_numeric_vector" /> </param> </when> <when value="regex" > <param name="selector" type="text" value="" label="Regular Expression to select gene names" > <expand macro="sanitize_regex" /> </param> </when> <when value="manual" > <param name="selector" type="text" value="" label="List of genes" > <expand macro="sanitize_string_vector" /> </param> </when> </conditional> </section> </macro> <!-- Sanitizers --> <macro name="sanitize_title"> <sanitizer invalid_char=""> <valid initial="string.letters,string.digits" > <add value=" " /> <add value="_" /> </valid> </sanitizer> </macro> <macro name="sanitize_regex" > <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"> <add value="!"/> <add value="="/> <add value="-"/> <add value="."/> <add value="*"/> <add value="?"/> <add value="+"/> <add value="\\"/> <add value="_"/> <add value="|"/> <add value="["/> <!-- left square bracket, e.g subselecting from vec[1] --> <add value="]"/> <!-- right square bracket --> <add value="("/> <!-- left parenthesis --> <add value=")"/> <!-- right parenthesis --> </valid> </sanitizer> </macro> <macro name="sanitize_numeric_vector" > <sanitizer invalid_char=""> <valid initial="string.digits"> <add value=","/> </valid> </sanitizer> </macro> <macro name="sanitize_string_vector" > <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"> <add value=","/> <add value="_"/> <add value="-"/> <add value="."/> </valid> </sanitizer> </macro> </macros>