diff r-sleuth.xml @ 3:172091d47f5a draft default tip

planemo upload for repository https://github.com/youyuh48/galaxy-sleuth/tree/master/ commit 8d9ff6181e933951e015e67f1719588bab2b3ab5-dirty

--- a/r-sleuth.xml	Fri Dec 08 22:15:41 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,79 +0,0 @@
-<tool id="r-sleuth" name="r-sleuth" version="0.29.0">
-  <description>Sleuth is an R library for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto.</description>
-  <requirements>
-    <requirement type="package" version="1.20.0">r-getopt</requirement>
-    <requirement type="package" version="0.29.0">r-sleuth</requirement>
-    <requirement type="package" version="2.34.0">bioconductor-biomart</requirement>
-  </requirements>
-  <version_command>
-    <![CDATA[
-      echo $(R --version | grep version | grep -v GNU)", r-sleuth version" $(R --vanilla --slave -e "library(sleuth); cat(sessionInfo()\$otherPkgs\$sleuth\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
-    ]]>
-  </version_command>
-  <command detect_errors="aggressive">
-    <![CDATA[
-      #import re
-      ## create symlinks to input datasets
-      #for $file in $input_files
-        #set $sname = re.sub('\.h5$', '', str($file.element_identifier))
-        mkdir -p 'data/${sname}/kallisto' &&
-        ln -s '$file' 'data/${sname}/kallisto/abundance.h5' &&
-      #end for
-
-      Rscript '${__tool_directory__}/r-sleuth.R'
-        --indir 'data'
-        --metadata '$metadata'
-        --full_model '~${full_model}'
-        --reduced_model '~${reduced_model}'
-        --gene_anno_name 'hsapiens_gene_ensembl' &&
-      tar zcvf sleuth_shiny.tar.gz data/app.R data/so.rds
-    ]]>
-  </command>
-  <inputs>
-    <param name="input_files" type="data" format="h5" label="Select Abundance(HDF5) Datasets" min="2" multiple="True"/>
-    <param name="metadata" type="data" format="txt,tsv,tabular" label="Metadata file"/>
-    <param name="full_model" type="text" value="condition" label="Full model"/>
-    <param name="reduced_model" type="text" value="1" label="Reduced model"/>
-    <param name="gene_anno_name" type="select" label="BioMart dataset">
-      <option value="hsapiens_gene_ensembl" selected="true">homo_sapiens</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="output" format="tar" label="${tool.name} on ${on_string}: R Shiny app" from_work_dir="sleuth_shiny.tar.gz"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input_files" value="SRR1867792.h5,SRR1909613.h5,SRR1909637.h5"/>
-      <param name="metadata" value="metadata.txt"/>
-      <output name="output" file="sleuth_shiny.tar.gz" ftype="tar"/>
-    </test>
-  </tests>
-  <help>
-<![CDATA[
-This is a Galaxy wrapper for the Sleuth package.
-
-**Input file format of metadata**
-
-sample      condition
----------------------
-SRR1867792  ESC
-SRR1909613  BM-MSC
-SRR1909637  BM-MSC
-
-**Output**
-
-This wrapper script generates Shiny web application files for RStudio.
-Unzip sleuth_shiny.tar.gz file, then run app.R file in RStudio.
-]]>
-  </help>
-  <citations>
-    <citation type="bibtex">
-      @misc{githubsleuth,
-      title = {sleuth},
-      publisher = {GitHub},
-      journal = {GitHub repository},
-      url = {https://pachterlab.github.io/sleuth/},
-      }
-    </citation>
-  </citations>
-</tool>