Mercurial > repos > nilesh > rseqc
annotate clipping_profile.xml @ 54:5873cd7afb67 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 62a9135bf04aec398d3172d17ccd60f5242d8e82
author | iuc |
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date | Wed, 13 Jun 2018 18:02:25 -0400 |
parents | 09846d5169fa |
children | dbedfc5f5a3c |
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09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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1 <tool id="rseqc_clipping_profile" name="Clipping Profile" version="@WRAPPER_VERSION@"> |
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2 <description> |
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3 estimates clipping profile of RNA-seq reads from BAM or SAM file |
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4 </description> |
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5 |
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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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9 |
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09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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10 <expand macro="requirements" /> |
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11 |
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12 <expand macro="stdio" /> |
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13 |
6b33e31bda10
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14 <version_command><![CDATA[clipping_profile.py --version]]></version_command> |
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15 |
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16 <command><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
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17 clipping_profile.py -i '${input}' -o output -q ${mapq} -s "${layout}" |
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18 ]]> |
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19 </command> |
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20 |
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21 <inputs> |
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09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
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22 <expand macro="bam_param" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
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23 <expand macro="mapq_param" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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24 <expand macro="layout_param" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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25 <expand macro="rscript_output_param" /> |
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26 </inputs> |
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27 |
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28 <outputs> |
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09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
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29 <expand macro="pdf_output_data" filename="output.clipping_profile.pdf" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
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30 <expand macro="xls_output_data" filename="output.clipping_profile.xls" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
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31 <expand macro="rscript_output_data" filename="output.clipping_profile.r" /> |
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32 </outputs> |
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33 |
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34 <tests> |
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Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
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35 <test> |
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09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
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36 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
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37 <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
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38 <output name="outputxls" file="output.clipping_profile.xls" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
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39 </test> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
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40 <test> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
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41 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
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42 <param name="rscript_output" value="true" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
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43 <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
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44 <output name="outputxls" file="output.clipping_profile.xls" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
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45 <output name="outputr" file="output.clipping_profile.r" /> |
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46 </test> |
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47 </tests> |
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48 |
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49 <help><![CDATA[ |
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50 clipping_profile.py |
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51 +++++++++++++++++++ |
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52 |
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53 This program is used to estimate clipping profile of RNA-seq reads from BAM or SAM file. |
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54 Note that to use this funciton, CIGAR strings within SAM/BAM file should have 'S' operation |
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55 (This means your reads aligner should support clipped mapping). |
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56 |
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57 Inputs |
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58 ++++++++++++++ |
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59 |
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60 Input BAM/SAM file |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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61 Alignment file in BAM/SAM format. |
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62 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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63 Minimum mapping quality |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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64 Minimum mapping quality for an alignment to be considered as "uniquely |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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65 mapped". default=30 |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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66 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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67 Sequencing layout |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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68 Denotes whether the sequecing was single-end (SE) or paired-end (PE). |
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69 |
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70 Sample Output |
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71 ++++++++++++++ |
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72 |
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73 .. image:: $PATH_TO_IMAGES/clipping_good.png |
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74 :height: 600 px |
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75 :width: 600 px |
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76 :scale: 80 % |
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77 |
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78 @ABOUT@ |
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79 |
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80 ]]> |
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81 </help> |
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82 |
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83 <expand macro="citations" /> |
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84 |
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85 </tool> |