changeset 2:20ec104b10be draft

Deleted selected files

--- a/c_rpkm.xml	Mon Feb 06 10:44:33 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-<tool id="conifer_rpkm" name="CoNIFER RPKM and Analyze" version="1.0">
-  <description></description>
-  <command>
-     mkdir rpkm_dir;
-#for $input_bam in $inputs:
-	#if str($input_bam.label.value) != "":
-	     ln -s ${input_bam.inputFile} ${$input_bam.label.value}.bam;
-	     ln -s ${input_bam.inputFile.metadata.bam_index} ${$input_bam.label.value}.bam.bai;
-	     python conifer.py rpkm 
-	     --probes $probesFile 
-	     --input ${$input_bam.label.value}.bam
-	     --output rpkm_dir/${$input_bam.label.value}.txt;
-	#else
-	     ln -s ${input_bam.inputFile} ${input_bam.inputFile.dataset.name}.bam;
-	     ln -s ${input_bam.inputFile.metadata.bam_index} ${input_bam.inputFile.dataset.name}.bam.bai;
-	     python conifer.py rpkm 
-	     --probes $probesFile 
-	     --input ${input_bam.inputFile.dataset.name}.bam
-	     --output rpkm_dir/${input_bam.inputFile.dataset.name}.txt;
-	#end if
-#end for
-     python conifer.py analyze 
-     --probes $probesFile 
-     --rpkm_dir rpkm_dir  
-     --output $outputFile 
-     --svd $svd 
-     2&gt;&amp;1;
-  </command>
-  <inputs>
-    <param format="bed" name="probesFile" type="data" label="Target regions (BED)" />
-    <repeat name="inputs" title="BAM" min="2" help="Need to add more files? Use controls below.">
-      <param format="bam" name="inputFile" type="data" label="BAM file" />
-      <param name="label" type="text" size="30" value="" label="Label" help="Label to use in the output. If not given, the dataset name will be used instead">
-        <validator type="regex" message="Spaces are not allowed">^\S*$</validator>
-      </param>
-    </repeat>
-    <param name="svd" type="integer" value="2" label="SVD" />
-  </inputs>
-  <outputs>
-    <data format="hdf5" name="outputFile" label="${tool.name} on ${on_string}: hdf5" />
-  </outputs>
-  <help>
-
-.. class:: warningmark
-
-**Warning about SVD**
-
-The SVD value must be less than the number of samples.
-
-E.g.: if the number of samples is 3, the value of SVD must be 2 or less.
-
-**What it does**
-
-This tool calculates RPKM for each BAM file and analyzes them, afterward it creates a unique HDF5 file containing all SVD-ZRPKM values,
-probes and samples for downstream analysis with 'CoNIFER CNV caller' and 'CoNIFER plot'.
-
-**License and citation**
-
-This Galaxy tool is Copyright © 2015 `CRS4 Srl.`_ and is released under the `MIT license`_.
-
-.. _CRS4 Srl.: http://www.crs4.it/
-.. _MIT license: http://opensource.org/licenses/MIT
-
-You can use this tool only if you agree to the license terms of: `CoNIFER`_.
-
-.. _CoNIFER: http://conifer.sourceforge.net/
-
-If you use this tool, please cite:
-
-- |Cuccuru2014|_
-- |Krumm2012|_.
-
-.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
-.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
-.. |Krumm2012| replace::  Krumm, N., Sudmant, P. H., Ko, A., O'Roak, B. J., Malig, M., Coe, B. P., NHLBI Exome Sequencing Project, Quinlan, A. R., Nickerson, D. A., Eichler, E. E. (2012) Copy number variation detection and genotyping from exome sequence data. *Genome Res.* 22(8), 1525-1532
-.. _Krumm2012: http://genome.cshlp.org/content/22/8/1525
-  </help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btu135</citation>
-    <citation type="doi">10.1101/gr.138115.112</citation>
-  </citations>
-</tool>