Mercurial > repos > jvolkening > b2b_count_mapped_reads
annotate count_mapped_reads.xml @ 1:a7ff53aff57b draft default tip
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
| author | jvolkening |
|---|---|
| date | Fri, 08 Mar 2024 00:55:24 +0000 |
| parents | 90d81e551420 |
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| rev | line source |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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1 <tool id="b2b_count_mapped_reads" name="Count mapped reads" version="0.001"> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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3 <description>Count reads uniquely mapped to each reference sequence</description> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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5 <!-- ***************************************************************** --> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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7 <requirements> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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8 <!-- ncurses needs to be explicitly pulled from conda-forge for samtools to work --> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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9 <requirement type="package" version="6.1">ncurses</requirement> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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10 <requirement type="package" version="1.9">samtools</requirement> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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11 </requirements> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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13 <!-- ***************************************************************** --> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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14 |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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15 <version_command>echo "0.001"</version_command> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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16 |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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17 <!-- ***************************************************************** --> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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19 <command detect_errors="aggressive"> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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20 <![CDATA[ |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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21 |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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22 #if $uniq: |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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23 samtools view -F 0x04 -F 0x100 -F 0x800 $in |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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24 #else |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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25 samtools view -F 0x04 $in |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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26 #end if |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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27 | cut -f3 |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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28 | sort |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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29 | uniq -c |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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30 | awk -v OFS='\t' '{print $2,$1}' |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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31 > $out |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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32 |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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33 ]]> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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34 </command> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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35 |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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36 <!-- ***************************************************************** --> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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37 |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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38 <inputs> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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39 <param name="in" type="data" format="bam" label="Read mapping" help="BAM format" /> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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40 <param name="uniq" type="boolean" checked="True" label="Exclude ambiguous mappings" /> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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41 </inputs> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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42 |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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43 <!-- ***************************************************************** --> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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44 |
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90d81e551420
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45 <outputs> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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46 <data name="out" format="tabular" label="Read counts" /> |
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47 </outputs> |
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48 |
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49 <!-- ***************************************************************** --> |
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50 |
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51 <tests> |
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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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52 <test> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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53 <param name="in" value="b2c.bam" ftype="bam" /> |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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54 <output name="out" file="b2c.counts" compare="diff" /> |
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55 </test> |
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90d81e551420
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56 </tests> |
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90d81e551420
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57 |
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58 <!-- ***************************************************************** --> |
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59 |
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90d81e551420
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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60 <help> |
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90d81e551420
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61 |
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90d81e551420
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62 `count_mapped_reads` is a Galaxy-only utility from BASE2BIO that simply |
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90d81e551420
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63 reports the number of reads mapped to each sequence from a BAM input file. |
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90d81e551420
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64 |
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65 </help> |
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66 |
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67 <!-- ***************************************************************** --> |
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68 |
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69 <citations> |
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70 </citations> |
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71 |
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72 </tool> |