Mercurial > repos > iuc > bctools_extract_crosslinked_nucleotides
annotate coords2clnt.xml @ 4:fc8e58d425d7 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a6a6774ae353f915a5ca34af8f281edd91e5c665
| author | iuc |
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| date | Fri, 04 Oct 2024 08:56:14 +0000 |
| parents | a2b091145fe0 |
| children |
| rev | line source |
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4
fc8e58d425d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a6a6774ae353f915a5ca34af8f281edd91e5c665
iuc
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1 <tool id="bctools_extract_crosslinked_nucleotides" name="Get crosslinked nucleotides" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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2 <description>from full alignments</description> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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3 <macros> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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4 <import>macros.xml</import> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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5 </macros> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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6 <expand macro="requirements"/> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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7 <command detect_errors="exit_code"><![CDATA[ |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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8 coords2clnt.py |
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a2b091145fe0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 513a54a013c5762aa6099fe044b2d3acf4a76881
iuc
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9 $threeprime |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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10 '$alignment_coordinates' |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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11 > '$crosslinking_coordinates' |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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12 ]]></command> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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13 <inputs> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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14 <param name="alignment_coordinates" type="data" format="bed" label="Alignments in BED format"/> |
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a2b091145fe0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 513a54a013c5762aa6099fe044b2d3acf4a76881
iuc
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15 <param argument="--threeprime" type="boolean" truevalue="--threeprime" falsevalue="" checked="false" |
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a2b091145fe0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 513a54a013c5762aa6099fe044b2d3acf4a76881
iuc
parents:
0
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16 label="Set position one nt downstream of 3'-end as crosslinked nucleotide" |
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a2b091145fe0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 513a54a013c5762aa6099fe044b2d3acf4a76881
iuc
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0
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17 help="Set position one nt downstream of 3'-end as crosslinked nucleotide. By default the crosslink site will be assumed to be one nt upstream of the 5'-end of the read."/> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
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18 </inputs> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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19 <outputs> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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20 <data name="crosslinking_coordinates" format="bed"/> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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21 </outputs> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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22 <tests> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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23 <test> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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24 <param name="alignment_coordinates" value="merged_pcr_dupes.bed"/> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
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changeset
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25 <output name="crosslinking_coordinates" file="merged_pcr_dupes_clnts.bed"/> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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diff
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26 </test> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff
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27 </tests> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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28 <help><![CDATA[ |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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29 |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
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changeset
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30 bctools - Get crosslinked nucleotides from full alignments |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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31 ========================================================== |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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32 |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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33 Given coordinates of aligned reads in BED format, calculate positions of the |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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34 crosslinked nucleotides. Crosslinked nts are assumed to be one nt upstream of |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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35 the 5'-end of the read. |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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36 |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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37 Input |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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38 ----- |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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39 |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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40 * six column BED file containing coordinates of aligned reads |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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41 |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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42 Output |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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43 ------ |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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44 |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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45 * six column BED file containing coordinates of crosslinking events |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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46 |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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47 ]]></help> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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48 <expand macro="citations"/> |
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07450cfb7de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
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49 </tool> |