Mercurial > repos > nilesh > rseqc

annotate mismatch_profile.xml @ 14:b21f0167e197 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec
author iuc
date Wed, 22 Feb 2023 15:05:13 +0000
parents a7f9084572fe
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1 <tool id="rseqc_mismatch_profile" name="Mismatch 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 mismatches across reads
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4 </description>
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5 <macros>
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6 <import>rseqc_macros.xml</import>
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7 </macros>
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8 <expand macro="bio_tools"/>
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10 <expand macro="requirements" />
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12 <expand macro="stdio" />
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14 <version_command><![CDATA[mismatch_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 mismatch_profile.py -i 'input.${extension}' -o output -l ${read_align_length} -n ${read_num} -q ${mapq}
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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_param" />
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24 <expand macro="readlength_param" />
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25 <expand macro="readnum_param" />
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26 <expand macro="mapq_param" />
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27 <expand macro="rscript_output_param" />
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28 </inputs>
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30 <outputs>
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31 <expand macro="pdf_output_data" filename="output.mismatch_profile.pdf" />
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32 <expand macro="xls_output_data" filename="output.mismatch_profile.xls" />
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33 <expand macro="rscript_output_data" filename="output.mismatch_profile.r" />
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34 </outputs>
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36 <tests>
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37 <test>
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38 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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39 <param name="read_align_length" value="101" />
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40 <param name="rscript_output" value="true" />
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41 <output name="outputpdf" file="output.mismatch_profile.pdf" compare="sim_size" />
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42 <output name="outputxls" file="output.mismatch_profile.xls" ftype="tabular"/>
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43 <output name="outputr" file="output.mismatch_profile_r"/>
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44 </test>
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45 </tests>
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47 <help><![CDATA[
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48 mismatch_profile.py
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49 +++++++++++++++++++
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51 Calculate the distribution of mismatches across reads.
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53 Note that the “MD” tag must exist in BAM file.
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55 Inputs
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56 ++++++
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58 Input BAM/SAM file
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59 Alignment file in BAM/SAM format.
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61 Alignment length of read
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62 It is usually set to the orignial read length. For example, all these cigar
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63 strings ("101M", "68M140N33M", "53M1D48M") suggest the read alignment
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64 length is 101. [required]
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66 Number of aligned reads used
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67 Number of aligned reads with deletions used to calculate the deletion
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68 profile. default=1000000
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70 Minimum mapping quality
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71 Minimum mapping quality for an alignment to be considered as "uniquely
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72 mapped". default=30
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74 Sample Output
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75 ++++++++++++++
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77 .. image:: $PATH_TO_IMAGES/mismatch_profile.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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82 @ABOUT@
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84 ]]>
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86 </help>
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88 <expand macro="citations" />
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90 </tool>