Mercurial > repos > nilesh > rseqc

annotate RNA_fragment_size.xml @ 56:daae0a118c36 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 62d3a29f93f3f6cb3ba9683fde5ff0606b90700d
author iuc
date Tue, 18 Sep 2018 09:11:06 -0400
parents 5873cd7afb67
children dbedfc5f5a3c
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1 <tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@WRAPPER_VERSION@.1">
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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">
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39 <assert_contents>
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40 <has_line_matching expression="^chrom\ttx_start\ttx_end\tsymbol\tfrag_count\tfrag_mean\tfrag_median\tfrag_std$" />
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41 <has_line_matching expression="^chr1\t11873\t14409\tNR_046018\t1\t0\t0\t0$" />
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42 <has_line_matching expression="^chr1\t14361\t29370\tNR_024540\t14\t66.5\t51.0\t41.119599080\d+$" />
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43 <has_line_matching expression="^chr1\t17368\t17436\tNR_106918\t0\t0\t0\t0$" />
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44 <has_line_matching expression="^chr1\t17368\t17436\tNR_107062\t0\t0\t0\t0$" />
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45 <has_line_matching expression="^chr1\t34610\t36081\tNR_026818\t0\t0\t0\t0$" />
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46 <has_line_matching expression="^chr1\t34610\t36081\tNR_026820\t0\t0\t0\t0$" />
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47 <has_line_matching expression="^chr1\t69090\t70008\tNM_001005484\t0\t0\t0\t0$" />
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48 </assert_contents>
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49 </output>
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50 </test>
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51 </tests>
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53 <help><![CDATA[
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54 RNA_fragment_size.py
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55 ++++++++++++++++++++
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57 Calculate fragment size for each gene/transcript. For each transcript, it will
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58 report : 1) Number of fragment that was used to estimate mean, median, std (see
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59 below). 2) mean of fragment size 3) median of fragment size 4) stdev of fragment
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60 size.
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62 Inputs
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63 ++++++
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65 Input BAM/SAM file
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66 Alignment file in BAM/SAM format.
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67
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68 Reference gene model
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69 Reference gene model in BED format. Must be strandard 12-column BED file.
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70 [required]
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72 Minimum mapping quality
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73 Minimum mapping quality for an alignment to be considered as "uniquely
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74 mapped". default=30
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75
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76 Minimum number of fragments
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77 Minimum number of fragments. default=3
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79 @ABOUT@
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81 ]]>
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83 </help>
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85 <expand macro="citations" />
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87 </tool>