comparison construct_eset.xml @ 1:be91cb6f48e7 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"

0:2cfd0db49bbc

        <configfile name="conf" >

suppressWarnings(suppressPackageStartupMessages(library(xbioc)))
suppressWarnings(suppressPackageStartupMessages(library(MuSiC)))

null_str_vec = function(gstr){
   tokens = unlist(as.vector(strsplit(gstr, split=",")))
   if (length(tokens) == 0){
      return(NULL)
   }
   if (length(tokens) == 1){
      return(tokens[[1]])
   }

pdata_file = '$pdata_file'
pdata = read.table(pdata_file, row.names = 1, header = T, sep = "\t", as.is=T)
#end if
## Annotation and Feature Data, or just a string for type of chip used
annotation = null_str_vec('$annotation')

if (all(rownames(pdata) != colnames(exprs))) {
   stop("Number of Samples between phenotypes and assays are not the same")
}

rownames(metadata) = unlist(metadata\$lname)
metadata\$ldesc = NULL
metadata\$lname = NULL

if (nrow(metadata)==0) {
   metadata = NULL
}

pheno_data = new("AnnotatedDataFrame", data = pdata, varMetadata = metadata)

## Experiment Description -- using the MIAME object
experiment_data = new(
    "MIAME",
    name = null_str_vec('$expdata.name'),
    lab = null_str_vec('$expdata.lab'),
    contact = null_str_vec('$expdata.contact'),
    title = null_str_vec('$expdata.title'),
    abstract = null_str_vec('$expdata.abstract'),
    url = null_str_vec('$expdata.url'),
    other = list(
#for i, row in enumerate($expdata.other):
    #if i==0
    '$row.field' = null_str_vec('$row.comment')
    #else
    ,'$row.field' = null_str_vec('$row.comment')
    #end if
#end for
))

e_set = ExpressionSet(assayData = exprs,
                      phenoData = pheno_data,
                      experimentData = experiment_data,
                      annotation = annotation)

capture.output(print(e_set), file = '$out_tab')
saveRDS(e_set, file= '$out_rds')

        </configfile>
    </configfiles>
    <inputs>

               optional="true" help="A string detailing which chip was used"  >
            <expand macro="validator_text_and_urls" />
        </param>
        <repeat name="metadata" title="Meta Data" min="0" max="15" >
            <!-- optional, so min=0 -->
            <param name="row_names" label="Label" type="text" >
                <expand macro="validator_text_and_urls" />
            </param>
            <param name="label_desc" label="Label Description" type="text" >
                <expand macro="validator_text_and_urls" />
            </param>

                </param>
            </repeat>
        </section>
    </inputs>
    <outputs>
        <data name="out_tab" format="tabular" label="${tool.name} on ${on_string}: General Info" />
        <data name="out_rds" format="rdata.eset" label="${tool.name} on ${on_string}: RData ESet Object" />
    </outputs>
    <tests>
        <test expect_num_outputs="2" >
            <!-- Values from the manual -->

                <repeat name="other" >
                    <param name="field" value="general" />
                    <param name="comment" value="Some other comment" />
                </repeat>
            </section>
            <output name="out_tab">
                <assert_contents>
                    <has_text text="assayData: 3 features, 2 samples " />
                </assert_contents>
            </output>
        </test>

1:be91cb6f48e7

        <configfile name="conf" >

suppressWarnings(suppressPackageStartupMessages(library(xbioc)))
suppressWarnings(suppressPackageStartupMessages(library(MuSiC)))

null_str_vec = function(gstr, is.str=FALSE){
   tokens = unlist(as.vector(strsplit(gstr, split=",")))
   if (length(tokens) == 0){
      if (is.str){
         return(character(0))
      }
      return(NULL)
   }
   if (length(tokens) == 1){
      return(tokens[[1]])
   }

pdata_file = '$pdata_file'
pdata = read.table(pdata_file, row.names = 1, header = T, sep = "\t", as.is=T)
#end if
## Annotation and Feature Data, or just a string for type of chip used
annotation = null_str_vec('$annotation')
if (is.null(annotation)){
   annotation = character(0)
}

if (all(rownames(pdata) != colnames(exprs))) {
   stop("Number of Samples between phenotypes and assays are not the same")
}

rownames(metadata) = unlist(metadata\$lname)
metadata\$ldesc = NULL
metadata\$lname = NULL

if (nrow(metadata)==0) {
    pheno_data = new("AnnotatedDataFrame", data = pdata)
} else {
    pheno_data = new("AnnotatedDataFrame", data = pdata, varMetadata = metadata)
}


## Experiment Description -- using the MIAME object
experiment_data = new(
    "MIAME",
    name = null_str_vec('$expdata.name', is.str=T),
    lab = null_str_vec('$expdata.lab', is.str=T),
    contact = null_str_vec('$expdata.contact', is.str=T),
    title = null_str_vec('$expdata.title', is.str=T),
    abstract = null_str_vec('$expdata.abstract', is.str=T),
    url = null_str_vec('$expdata.url', is.str=T),
    other = list(
#for i, row in enumerate($expdata.other):
    #if i==0
    '$row.field' = null_str_vec('$row.comment', is.str=T)
    #else
    ,'$row.field' = null_str_vec('$row.comment', is.str=T)
    #end if
#end for
))

e_set = ExpressionSet(assayData = exprs,
                      phenoData = pheno_data,
                      experimentData = experiment_data,
                      annotation = annotation)

capture.output(print(e_set), file = '$out_txt')
saveRDS(e_set, file= '$out_rds')

        </configfile>
    </configfiles>
    <inputs>

               optional="true" help="A string detailing which chip was used"  >
            <expand macro="validator_text_and_urls" />
        </param>
        <repeat name="metadata" title="Meta Data" min="0" max="15" >
            <!-- optional, so min=0 -->
            <param name="row_names" label="Label" type="text"
                   help="Metadata should correspond directly to the columns of the Phenotype Data" >
                <expand macro="validator_text_and_urls" />
            </param>
            <param name="label_desc" label="Label Description" type="text" >
                <expand macro="validator_text_and_urls" />
            </param>

                </param>
            </repeat>
        </section>
    </inputs>
    <outputs>
        <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: General Info" />
        <data name="out_rds" format="rdata.eset" label="${tool.name} on ${on_string}: RData ESet Object" />
    </outputs>
    <tests>
        <test expect_num_outputs="2" >
            <!-- Values from the manual -->

                <repeat name="other" >
                    <param name="field" value="general" />
                    <param name="comment" value="Some other comment" />
                </repeat>
            </section>
            <output name="out_txt">
                <assert_contents>
                    <has_text text="assayData: 3 features, 2 samples " />
                </assert_contents>
            </output>
        </test>