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annotate RNA_fragment_size.xml @ 63:27e16a30667a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
author iuc
date Tue, 09 Apr 2024 11:24:55 +0000
parents 5968573462fa
children
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1 <tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_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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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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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <version_command><![CDATA[RNA_fragment_size.py --version]]></version_command>
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12 <command><![CDATA[
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13 @BAM_SAM_INPUTS@
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14 RNA_fragment_size.py -i 'input.${extension}' --refgene='${refgene}' --mapq=${mapq} --frag-num=${fragnum} > '${output}'
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15 ]]>
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16 </command>
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17 <inputs>
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18 <expand macro="bam_param"/>
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19 <expand macro="refgene_param"/>
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20 <expand macro="mapq_param"/>
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21 <param name="fragnum" type="integer" value="3" label="Minimum number of fragments (default: 3)" help="(--frag-num)"/>
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22 </inputs>
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23 <outputs>
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24 <data format="tabular" name="output"/>
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25 </outputs>
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26 <tests>
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27 <test expect_num_outputs="1">
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28 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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29 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
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30 <output name="output">
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31 <assert_contents>
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32 <has_line_matching expression="^chrom\ttx_start\ttx_end\tsymbol\tfrag_count\tfrag_mean\tfrag_median\tfrag_std$"/>
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33 <has_line_matching expression="^chr1\t11873\t14409\tNR_046018\t1\t0\t0\t0$"/>
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34 <has_line_matching expression="^chr1\t14361\t29370\tNR_024540\t14\t66.5\t51.0\t41.119599080\d+$"/>
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35 <has_line_matching expression="^chr1\t17368\t17436\tNR_106918\t0\t0\t0\t0$"/>
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36 <has_line_matching expression="^chr1\t17368\t17436\tNR_107062\t0\t0\t0\t0$"/>
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37 <has_line_matching expression="^chr1\t34610\t36081\tNR_026818\t0\t0\t0\t0$"/>
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38 <has_line_matching expression="^chr1\t34610\t36081\tNR_026820\t0\t0\t0\t0$"/>
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39 <has_line_matching expression="^chr1\t69090\t70008\tNM_001005484\t0\t0\t0\t0$"/>
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40 </assert_contents>
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41 </output>
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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45 RNA_fragment_size.py
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46 ++++++++++++++++++++
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48 Calculate fragment size for each gene/transcript. For each transcript, it will
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49 report : 1) Number of fragment that was used to estimate mean, median, std (see
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50 below). 2) mean of fragment size 3) median of fragment size 4) stdev of fragment
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51 size.
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53 Inputs
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54 ++++++
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56 Input BAM/SAM file
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57 Alignment file in BAM/SAM format.
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59 Reference gene model
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60 Reference gene model in BED format. Must be strandard 12-column BED file.
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61 [required]
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63 Minimum mapping quality
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64 Minimum mapping quality for an alignment to be considered as "uniquely
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65 mapped". default=30
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67 Minimum number of fragments
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68 Minimum number of fragments. default=3
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70 @ABOUT@
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72 ]]>
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74 </help>
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75 <expand macro="citations"/>
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76 </tool>