Mercurial > repos > artbio > pindel
annotate pindelwrapper.xml @ 1:078c6ab38858 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 90fe127eb55d6ec4f99a37f7049527b6898e66a4
author | artbio |
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date | Tue, 13 Feb 2024 10:53:40 +0000 |
parents | decc6b5631dc |
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rev | line source |
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1
078c6ab38858
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 90fe127eb55d6ec4f99a37f7049527b6898e66a4
artbio
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1 <tool id ="pindel" name="Pindel" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
0
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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2 <description></description> |
1
078c6ab38858
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 90fe127eb55d6ec4f99a37f7049527b6898e66a4
artbio
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3 <macros> |
078c6ab38858
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 90fe127eb55d6ec4f99a37f7049527b6898e66a4
artbio
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4 <token name="@TOOL_VERSION@">0.2.5b9</token> |
078c6ab38858
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 90fe127eb55d6ec4f99a37f7049527b6898e66a4
artbio
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0
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5 <token name="@VERSION_SUFFIX@">0</token> |
078c6ab38858
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 90fe127eb55d6ec4f99a37f7049527b6898e66a4
artbio
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6 <token name="@PROFILE@">23.0</token> |
078c6ab38858
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 90fe127eb55d6ec4f99a37f7049527b6898e66a4
artbio
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0
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7 </macros> |
0
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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8 <requirements> |
1
078c6ab38858
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 90fe127eb55d6ec4f99a37f7049527b6898e66a4
artbio
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0
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9 <requirement type="package" version="@TOOL_VERSION@">pindel</requirement> |
078c6ab38858
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 90fe127eb55d6ec4f99a37f7049527b6898e66a4
artbio
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10 <requirement type="package" version="1.19.2">samtools</requirement> |
078c6ab38858
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 90fe127eb55d6ec4f99a37f7049527b6898e66a4
artbio
parents:
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11 <requirement type="package" version="3.12.1">python</requirement> |
0
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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12 </requirements> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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13 <stdio> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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14 <exit_code range="1:" /> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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15 </stdio> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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16 <command><![CDATA[ |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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17 ln -f -s "$input_file.metadata.bam_index" alignment.sorted.bam.bai && |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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18 ln -f -s "$input_file" alignment.sorted.bam && |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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19 ln -f -s "$reference" ref.fa && |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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changeset
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20 samtools faidx ref.fa && |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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21 python $__tool_directory__/create_config_file.py |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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changeset
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22 --input_file alignment.sorted.bam |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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23 --insert_size "$insert_size" |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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24 --sample_label "$input_file.element_identifier" |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
changeset
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25 --output_config_file output_config_file && |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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26 pindel |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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27 -f ref.fa |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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28 -i output_config_file |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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29 -c "$chromosome" |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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30 -o prefix && |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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31 mv prefix_D $Deletions && |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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32 mv prefix_SI $Short_Insertions && |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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33 mv prefix_LI $Long_Insertions && |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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34 mv prefix_INV $Inversions && |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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35 mv prefix_TD $Tandem_Duplications && |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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36 mv prefix_RP $Read_Pair && |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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37 mv prefix_INT_final $int_final && |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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38 mv prefix_CloseEndMapped $Close_End_Mapped |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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39 ]]></command> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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40 <inputs> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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41 <param format="bam" name="input_file" type="data" label="One or more BAM alignment files produced by BWA"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
changeset
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42 <param name="insert_size" type="integer" value="" label="Expected Insert size" /> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
changeset
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43 <param format="fasta" name="reference" type="data" label="Reference genome in fasta format"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
changeset
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44 <param name="chromosome" type="text" value="ALL" help="Select a chromsome. ALL will use all chromosomes" |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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45 label="Which chromosome to operate on"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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46 </inputs> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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47 <outputs> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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48 <data format="txt" name="Deletions" label="${input_file.element_identifier} Deletions"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
changeset
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49 <data format="txt" name="Short_Insertions" label="${input_file.element_identifier} Short Insertions"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
changeset
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50 <data format="txt" name="Long_Insertions" label="${input_file.element_identifier} Long Insertions"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
changeset
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51 <data format="txt" name="Inversions" label="${input_file.element_identifier} Inversions"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
changeset
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52 <data format="txt" name="Tandem_Duplications" label="${input_file.element_identifier} Tandem Duplications"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
changeset
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53 <data format="txt" name="Breakpoints" label="${input_file.element_identifier} Breakpoints"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
changeset
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54 <data format="txt" name="Read_Pair" label="${input_file.element_identifier} Read Pair Evidence"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
changeset
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55 <data format="txt" name="int_final" label="${input_file.element_identifier} INT_final"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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56 <data format="txt" name="Close_End_Mapped" label="${input_file.element_identifier} Close End Mapped"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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57 </outputs> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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58 <tests> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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59 <test> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
changeset
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60 <param name="input_file" value="X_100000_Hum1.bam" ftype="bam"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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61 <param name="insert_size" value="250"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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62 <param name="reference" value="dm6_X.fasta" ftype="fasta"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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63 <param name="chromosome" value="ALL"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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64 <output name="Deletions" file="X_100000_Hum1.bam_Deletions.txt" ftype="txt"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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65 <output name="Short_Insertions" file="X_100000_Hum1.bam_Short_Insertions.txt" ftype="txt"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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66 <output name="Long_Insertions" file="X_100000_Hum1.bam_Long_Insertions.txt" ftype="txt"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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67 <output name="Inversions" file="X_100000_Hum1.bam_Inversions.txt" ftype="txt"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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68 <output name="Tandem_Duplications" file="X_100000_Hum1.bam_Tandem_Duplications.txt" ftype="txt"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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69 <output name="Breakpoints" file="X_100000_Hum1.bam_Breakpoints.txt" ftype="txt"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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70 <output name="Read_Pair" file="X_100000_Hum1.bam_Read_Pair_Evidence.txt" ftype="txt"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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71 <output name="int_final" file="X_100000_Hum1.bam_INT_final.txt" ftype="txt"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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72 <output name="Close_End_Mapped" file="X_100000_Hum1.bam_Close_End_Mapped.txt" ftype="txt"/> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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73 </test> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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74 </tests> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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75 <help> <![CDATA[ |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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76 |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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77 Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
diff
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78 tandem duplications and other structural variants at single-based resolution from |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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79 next-generation sequencing data. It uses a pattern growth approach to identify the |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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80 breakpoints of these variants from paired-end short reads. |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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81 |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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82 The following inputs/parameters are required: |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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83 - One or more BAM alignment files produced by BWA |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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84 - Expected Insert Size for each alignment file |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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85 - Sample label for each alignment file |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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86 - Reference genome in fasta format (the same one used in alignment) |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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87 - Which chromosome to operate on |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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88 |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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89 The following output files are produced by Pindel: |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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90 - Deletions |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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91 - Short Insertions |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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92 - Long Insertions |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
parents:
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93 - Inversions |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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94 - Tandom Duplications |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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95 - Breakpoints |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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96 - Read Pair Evidence |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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97 - INT_final |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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98 - Close End Mapped |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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99 |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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100 |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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101 ]]> </help> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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102 <citations> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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103 <citation type="doi">doi:10.1093/bioinformatics/btp394</citation> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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104 </citations> |
decc6b5631dc
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
artbio
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105 </tool> |