changeset 61:b5063e189f57 draft

Deleted selected files

--- a/picard_DownsampleSam.xml	Tue Feb 18 15:57:17 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-<tool name="Downsample SAM" id="picard_DownsampleSam" version="1.106.0">
-    <!-- found on https://bitbucket.org/bwlang/galaxy-dist/src/ca5ded2e18a9ef802c31429e3cb861e8775b24d0/tools/picard/picard_DownsampleSam.xml -->
-   <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
-  <command interpreter="python">
-    picard_wrapper.py
-      --input=$inputFile
-      --output=$outFile
-      --probability=$probability
-      --seed=$seed
-      -j "\$JAVA_JAR_PATH/DownsampleSam.jar"
-  </command>
-  <inputs>
-    <param format="sam" name="inputFile" type="data" label="SAM dataset to be downsampled"
-           help="If empty, upload or import a SAM dataset." />
-    <param name="probability" type="float" size="5" label="Probability (between 0 and 1) that any given read will be kept" help="specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" />
-    <param name="seed" type="integer" size="5" label="Random seed value" help="(same seed + same probability = same set of reads kept)" value="1" />
-
-  </inputs>
-  <outputs>
-    <data name="outFile" format="sam" label="${tool.name} on ${on_string}">
-    </data>
-  </outputs>
-  <tests>
-    <test>
-      <param name="inputFile" value="cleansamtestinput.sam" />
-      <param name="probability" value="0.1" />
-      <param name="seed" value="2" />
-      <output name="outFile" file="downsamplesamoutput.sam" ftype="sam" />
-    </test>
-  </tests>
-  <help>
-
-.. class:: infomark
-
-**Purpose**
-
-Randomly down-sample a SAM or BAM file to retain a random subset of the reads. Mate-pairs are either both kept or both discarded. Reads marked as not primary alignments are all discarded. Each read is given a probability P of being retained - results with the exact same input in the same order and with the same value for RANDOM_SEED will produce the same results.
-
-**Picard documentation**
-
-This is a Galaxy wrapper for DownsampleSam, a part of the external package Picard-tools_.
-
- .. _Picard-tools: http://www.google.com/search?q=picard+samtools
-
-------
-
-.. class:: warningmark
-
-**Warning on SAM/BAM quality**
-
-Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
-flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
-to be the only way to deal with SAM/BAM that cannot be parsed.
-
-
-  </help>
-</tool>
\ No newline at end of file