Mercurial > repos > nilesh > rseqc

annotate insertion_profile.xml @ 60:1421603cc95b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
author iuc
date Sat, 26 Nov 2022 15:19:14 +0000
parents dbedfc5f5a3c
children 5968573462fa
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1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
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1 <tool id="rseqc_insertion_profile" name="Insertion Profile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
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2 <description>
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3 calculates the distribution of inserted nucleotides across reads
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4 </description>
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5 <expand macro="bio_tools"/>
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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[insertion_profile.py --version]]></version_command>
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16 <command><![CDATA[
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17 @BAM_SAM_INPUTS@
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18 insertion_profile.py -i 'input.${extension}' -o output -q ${mapq} -s "${layout}"
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19 ]]>
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20 </command>
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22 <inputs>
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23 <expand macro="bam_sam_param" />
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24 <expand macro="mapq_param" />
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25 <expand macro="layout_param" />
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26 <expand macro="rscript_output_param" />
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27 </inputs>
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29 <outputs>
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30 <expand macro="pdf_output_data" filename="output.insertion_profile.pdf" />
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31 <expand macro="xls_output_data" filename="output.insertion_profile.xls" />
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32 <expand macro="rscript_output_data" filename="output.insertion_profile.r" />
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33 </outputs>
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35 <tests>
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36 <test>
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37 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
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38 <param name="rscript_output" value="true" />
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39 <output name="outputpdf" file="output.insertion_profile.pdf" compare="sim_size" />
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40 <output name="outputxls" file="output.insertion_profile.xls" />
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41 <output name="outputr" file="output.insertion_profile_r" />
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42 </test>
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43 </tests>
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45 <help><![CDATA[
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46 insertion_profile.py
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47 ++++++++++++++++++++
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49 Calculate the distributions of inserted nucleotides across reads. Note that to
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50 use this funciton, CIGAR strings within SAM/BAM file should have ‘I’ operation.
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52 Inputs
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53 ++++++
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55 Input BAM/SAM file
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56 Alignment file in BAM/SAM format.
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58 Minimum mapping quality
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59 Minimum mapping quality for an alignment to be considered as "uniquely
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60 mapped". default=30
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62 Sequencing layout
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63 Denotes whether the sequecing was single-end (SE) or paired-end (PE).
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65 Sample Output
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66 ++++++++++++++
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68 Read-1 insertion profile:
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70 .. image:: $PATH_TO_IMAGES/out.insertion_profile.R1.png
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71 :height: 600 px
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72 :width: 600 px
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73 :scale: 80 %
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75 Read-2 insertion profile:
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77 .. image:: $PATH_TO_IMAGES/out.insertion_profile.R2.png
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78 :height: 600 px
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79 :width: 600 px
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80 :scale: 80 %
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81
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82 @ABOUT@
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83
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84 ]]>
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85 </help>
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87 <expand macro="citations" />
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89 </tool>