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annotate RNA_fragment_size.xml @ 3:71ed55a3515a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
author iuc
date Tue, 14 Mar 2017 10:22:57 -0400
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71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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1 <tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@WRAPPER_VERSION@">
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2 <description>
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3 calculates the fragment size for each gene/transcript
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4 </description>
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6 <macros>
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7 <import>rseqc_macros.xml</import>
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8 </macros>
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10 <expand macro="requirements" />
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12 <expand macro="stdio" />
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14 <version_command><![CDATA[RNA_fragment_size.py --version]]></version_command>
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16 <command><![CDATA[
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17 ln -sf '${input}' 'input.bam' &&
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18 ln -sf '$input.metadata.bam_index' 'input.bam.bai' &&
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19 RNA_fragment_size.py -i 'input.bam' --refgene='${refgene}' --mapq=${mapq} --frag-num=${fragnum} > '${output}'
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20 ]]>
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21 </command>
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23 <inputs>
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24 <expand macro="bam_param" />
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25 <expand macro="refgene_param" />
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26 <expand macro="mapq_param" />
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27 <param name="fragnum" type="integer" value="3" label="Minimum number of fragments (default: 3)" help="(--frag-num)" />
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28 </inputs>
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30 <outputs>
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31 <data format="tabular" name="output" />
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32 </outputs>
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34 <tests>
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35 <test>
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36 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
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37 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" />
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38 <output name="output" file="output.RNA_fragment_size.txt" />
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39 </test>
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40 </tests>
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42 <help><![CDATA[
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43 RNA_fragment_size.py
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44 ++++++++++++++++++++
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46 Calculate fragment size for each gene/transcript. For each transcript, it will
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47 report : 1) Number of fragment that was used to estimate mean, median, std (see
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48 below). 2) mean of fragment size 3) median of fragment size 4) stdev of fragment
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49 size.
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51 Inputs
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52 ++++++
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54 Input BAM/SAM file
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55 Alignment file in BAM/SAM format.
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57 Reference gene model
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58 Reference gene model in BED format. Must be strandard 12-column BED file.
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59 [required]
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61 Minimum mapping quality
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62 Minimum mapping quality for an alignment to be considered as "uniquely
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63 mapped". default=30
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64
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65 Minimum number of fragments
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66 Minimum number of fragments. default=3
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68 @ABOUT@
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70 ]]>
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72 </help>
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74 <expand macro="citations" />
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76 </tool>