Mercurial > repos > iuc > crossmap_bam
annotate crossmap_bam.xml @ 10:5e3b182af35c draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e10d34b547557b2bd4f0be69e31204bd5703e422"
author | iuc |
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date | Thu, 20 Jan 2022 04:29:28 +0000 |
parents | c413cbb69f3c |
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rev | line source |
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acd53aae2d46
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
iuc
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1 <tool id="crossmap_bam" name="CrossMap BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> |
0
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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2 <description>Convert genome coordinates or annotation files between genome assemblies</description> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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3 <macros> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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4 <import>macros.xml</import> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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5 </macros> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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6 <expand macro="requirements"/> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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7 <expand macro="stdio"/> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
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8 <expand macro="version_command"/> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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9 <command><![CDATA[ |
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c76b5389bb34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
iuc
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10 |
c76b5389bb34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
iuc
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11 ln -s '${input}' ./input.bam && |
c76b5389bb34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
iuc
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12 |
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6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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13 CrossMap.py bam |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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14 '${chain_source.input_chain}' |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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15 $optional_tags |
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9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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16 |
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6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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17 -m $insert_size |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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18 -s $insert_size_stdev |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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19 -t $insert_size_fold |
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9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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20 |
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c76b5389bb34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
iuc
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21 ./input.bam |
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dde84a63f767
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
iuc
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22 output |
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9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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23 ]]></command> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
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24 <inputs> |
2
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents:
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25 <param name="input" type="data" format="bam" label="BAM file"/> |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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26 |
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9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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27 <expand macro="chain" /> |
2
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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28 |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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29 <param name="optional_tags" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Add optional BAM Headers"/> |
0
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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30 |
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6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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31 <param name="insert_size" argument="-m" type="float" value="200.0" label="Insert size" help="Average insert size of pair-end sequencing (bp)"/> |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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32 <param name="insert_size_stdev" argument="-s" type="float" value="30.0" label="Insert size std. dev" help="Stanadard deviation of insert size"/> |
5
c76b5389bb34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
iuc
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33 <param name="insert_size_fold" argument="-t" type="float" value="3.0" label="Insert size std. dev foldchange" |
c76b5389bb34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
iuc
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34 help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean"/> |
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6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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35 </inputs> |
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9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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36 |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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37 <outputs> |
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dde84a63f767
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
iuc
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38 <data name="output" format="bam" label="${tool.name} on ${on_string}" from_work_dir="output.sorted.bam" /> |
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6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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39 <!-- CrossMap 0.2.5 does not produce output_unmapped --> |
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9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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40 </outputs> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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41 |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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42 <tests> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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43 <test> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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44 <param name="index_source" value="history"/> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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45 <param name="input" value="test_bam_01_input_a.bam" ftype="bam"/> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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46 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
iuc
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47 <output name="output" file="test_bam_01_output_a.bam" ftype="bam" lines_diff="4" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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48 </test> |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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49 <test> |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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50 <param name="index_source" value="cached"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 39a5f30a013c6d71ea84807b72511e3aa4bab147
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51 <param name="input" value="test_bam_01_input_a.bam" ftype="bam" dbkey="hg18"/> |
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acd53aae2d46
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
iuc
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52 <output name="output" file="test_bam_01_output_a.bam" ftype="bam" lines_diff="4" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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53 </test> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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54 </tests> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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55 <help><![CDATA[ |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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56 @HELP_GENERAL@ |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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57 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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58 BAM |
0
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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59 --------- |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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60 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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61 CrossMap updates chromosomes, genome coordinates, header sections, and all |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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62 BAM flags accordingly. The program version (of CrossMap) is inserted into the |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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63 header section, along with the names of the original BAM file and the chain |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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64 file. For pair-end sequencing, insert size is also recalculated. |
0
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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65 |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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66 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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67 **Optional tags** |
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9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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68 |
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69 Q |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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70 QC. QC failed. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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71 |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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72 N |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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73 Unmapped. Originally unmapped or originally mapped but failed to liftover to new assembly. |
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9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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74 |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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75 M |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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76 Multiple mapped. Alignment can be liftover to multiple places. |
0
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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77 |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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78 U |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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79 Unique mapped. Alignment can be liftover to only 1 place. |
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9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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80 |
2
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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81 **Tags for pair-end sequencing include:** |
0
9bcfe0aabf5d
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82 |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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83 QF |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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84 QC failed |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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85 NN |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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86 both read1 and read2 unmapped |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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87 NU |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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88 read1 unmapped, read2 unique mapped |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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89 NM |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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90 read1 unmapped, multiple mapped |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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91 UN |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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92 read1 uniquely mapped, read2 unmap |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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93 UU |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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94 both read1 and read2 uniquely mapped |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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95 UM |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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96 read1 uniquely mapped, read2 multiple mapped |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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97 MN |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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98 read1 multiple mapped, read2 unmapped |
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99 MU |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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100 read1 multiple mapped, read2 unique mapped |
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101 MM |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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102 both read1 and read2 multiple mapped |
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9bcfe0aabf5d
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103 |
2
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104 **Tags for single-end sequencing include** |
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105 |
2
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106 QF |
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107 QC failed |
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108 SN |
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109 unmaped |
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110 SM |
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111 multiple mapped |
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112 SU |
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113 uniquely mapped |
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114 ]]></help> |
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115 |
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116 <citations> |
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117 <citation type="doi">10.1093/bioinformatics/btt730</citation> |
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118 </citations> |
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119 </tool> |