Mercurial > repos > devteam > bamtools
annotate bamtools.xml @ 7:ddb22028b552 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools commit 862f05b5053f55def8007194a702019418697cb5
author | iuc |
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date | Fri, 13 Jan 2023 12:17:31 +0000 |
parents | e4490b16f0d7 |
children | 970e6333f07e |
rev | line source |
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0 | 1 <?xml version="1.0"?> |
7
ddb22028b552
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools commit 862f05b5053f55def8007194a702019418697cb5
iuc
parents:
6
diff
changeset
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2 <tool id="bamtools" name="Operate on and transform BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
ddb22028b552
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools commit 862f05b5053f55def8007194a702019418697cb5
iuc
parents:
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diff
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3 <description>datasets in various ways</description> |
4
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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4 <macros> |
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
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diff
changeset
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5 <import>macros.xml</import> |
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
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diff
changeset
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6 </macros> |
6
e4490b16f0d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 29fe5251fcc37a22a1ce479d7a39f5007a4f02ec
iuc
parents:
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changeset
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7 <expand macro="requirements"> |
e4490b16f0d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 29fe5251fcc37a22a1ce479d7a39f5007a4f02ec
iuc
parents:
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8 <requirement type="package" version="1.16.1">samtools</requirement> |
e4490b16f0d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 29fe5251fcc37a22a1ce479d7a39f5007a4f02ec
iuc
parents:
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diff
changeset
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9 </expand> |
e4490b16f0d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 29fe5251fcc37a22a1ce479d7a39f5007a4f02ec
iuc
parents:
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10 <command detect_errors="exit_code"><![CDATA[ |
3
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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changeset
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11 ##set up input files |
4
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
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12 ln -s '${input_bams}' localbam.bam && |
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
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changeset
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13 ln -s '${input_bams.metadata.bam_index}' localbam.bam.bai && |
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
3
diff
changeset
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14 #if str( $analysis_type.analysis_type_selector ) == 'convert': |
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
3
diff
changeset
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15 #if str( $analysis_type.format_type.format_type_selector ) == 'pileup': |
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
3
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changeset
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16 #set $reference_fasta_filename = 'localref.fa' |
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
3
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changeset
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17 #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == 'history': |
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
3
diff
changeset
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18 ln -s '${analysis_type.format_type.reference_source.ref_file}' '${reference_fasta_filename}' && |
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
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diff
changeset
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19 samtools faidx '${reference_fasta_filename}' 2>&1 || echo 'Error running samtools faidx for bamtools convert' >&2 && |
3
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
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changeset
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20 #else: |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
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changeset
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21 #set $reference_fasta_filename = str( $analysis_type.format_type.reference_source.ref_file.fields.path ) |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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changeset
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22 #end if |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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changeset
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23 #end if |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
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changeset
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24 #end if |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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25 bamtools |
4
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
3
diff
changeset
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26 #if str( $analysis_type.analysis_type_selector ) == 'convert': |
3
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
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27 convert |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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28 -format ${analysis_type.format_type.format_type_selector} |
4
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
3
diff
changeset
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29 #if str( $analysis_type.format_type.format_type_selector ) == 'pileup': |
3
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
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30 ${analysis_type.format_type.mapqual} |
4
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
3
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31 -fasta '${reference_fasta_filename}' |
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
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32 #elif str( $analysis_type.format_type.format_type_selector ) == 'sam': |
3
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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changeset
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33 ${analysis_type.format_type.noheader} |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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34 #end if |
4
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
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35 -out '$out_file1' |
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
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36 #elif str( $analysis_type.analysis_type_selector ) == 'count': |
3
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
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37 count |
4
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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38 > '$out_file1' |
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
3
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changeset
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39 #elif str( $analysis_type.analysis_type_selector ) == 'coverage': |
3
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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changeset
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40 coverage |
4
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
3
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41 -out '$out_file1' |
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
3
diff
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42 #elif str( $analysis_type.analysis_type_selector ) == 'header': |
3
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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changeset
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43 header |
4
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
3
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44 > '$out_file1' |
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
3
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45 #elif str( $analysis_type.analysis_type_selector ) == 'merge': |
3
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
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46 merge |
4
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
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47 -out '$out_file1' |
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
3
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48 #elif str( $analysis_type.analysis_type_selector ) == 'random': |
3
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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diff
changeset
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49 random |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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50 -n ${analysis_type.count} |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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51 -seed ${analysis_type.seed} |
4
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
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52 -out '$out_file1' |
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
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53 #elif str( $analysis_type.analysis_type_selector ) == 'revert': |
3
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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54 revert |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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55 ${analysis_type.keepDuplicate} |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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56 ${analysis_type.keepQualities} |
4
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
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57 -out '$out_file1' |
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
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58 #elif str( $analysis_type.analysis_type_selector ) == 'sort': |
3
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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59 sort |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
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60 ${analysis_type.byname} |
4
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
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61 -out '$out_file1' |
3
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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62 #end if |
4
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
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63 -in localbam.bam |
6
e4490b16f0d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 29fe5251fcc37a22a1ce479d7a39f5007a4f02ec
iuc
parents:
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64 ]]></command> |
3
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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65 <inputs> |
4
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents:
3
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66 <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" /> |
3
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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changeset
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67 <conditional name="analysis_type"> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
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68 <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool"> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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69 <option value="convert">Convert</option> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
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70 <option value="count">Count</option> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
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71 <option value="coverage">Coverage</option> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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72 <option value="header">Header</option> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
73 <option value="merge">Merge</option> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
74 <option value="random">Random</option> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
75 <option value="revert">Revert</option> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
76 <!-- The sort option below is commented out as BAM files in Galaxy are reference sorted by dafault. --> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
77 <!-- Allowing users for sort files may break donstream functionality. --> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
78 <!-- To enable sort option simply uncomment the line below: --> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
79 <!-- <option value="sort">Sort</option> --> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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diff
changeset
|
80 </param> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
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81 <when value="convert"> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
82 <conditional name="format_type"> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
83 <param name="format_type_selector" type="select" help="Select what to convert your BAM to"> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
84 <option value="bed">BED</option> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
85 <option value="fasta">FASTA</option> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
86 <option value="fastq">FASTQ</option> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
87 <option value="json">JSON</option> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
88 <option value="pileup">Pileup</option> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
89 <option value="sam">SAM</option> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
90 <option value="yaml">YAML</option> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
91 </param> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
92 <when value="bed"/> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
93 <when value="fasta"/> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
94 <when value="fastq"/> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
95 <when value="json"/> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
96 <when value="yaml"/> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
97 <when value="pileup"> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
98 <conditional name="reference_source"> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
99 <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
100 <option value="cached">Locally cached</option> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
101 <option value="history">History</option> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
102 </param> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
103 <when value="cached"> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
104 <param name="ref_file" type="select" label="Using reference genome"> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
105 <options from_data_table="sam_fa_indexes"> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
106 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>--> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
107 </options> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
108 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
109 </param> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
110 </when> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
111 <when value="history"> <!-- FIX ME!!!! --> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
112 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
113 </when> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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diff
changeset
|
114 </conditional> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
115 <param name="mapqual" type="boolean" truevalue="-mapqual" falsevalue="" label="Print quality scores?" /> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
116 </when> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
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117 <when value="sam"> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
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118 <param name="noheader" type="boolean" truevalue="-noheader" falsevalue="" label="Do not print header" /> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
119 </when> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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diff
changeset
|
120 </conditional> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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diff
changeset
|
121 </when> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
122 <when value="count" /> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
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123 <when value="coverage" /> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
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124 <when value="header" /> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
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125 <when value="merge" /> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
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126 <when value="random"> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
127 <param name="count" type="integer" value="10000" label="Number of random alignments to grab" help="No duplicate checking is perfomed" /> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
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128 <param name="seed" type="integer" value="1024" label="Random number generator seed" help="Use the same seed for reproducible results" /> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
129 </when> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
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130 <when value="revert"> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
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131 <param name="keepDuplicate" type="boolean" truevalue="-keepDuplicate" falsevalue="" label="Keep duplicates marked" help="Do not remove duplicate marks" /> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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132 <param name="keepQualities" type="boolean" truevalue="-keepQualities" falsevalue="" label="Keep base qualities" help="Do not replace qualities with contect of OQ tag" /> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
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133 </when> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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diff
changeset
|
134 <!-- |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
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changeset
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135 <when value="sort"> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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changeset
|
136 <param name="byname" type="boolean" truevalue="-byname" falsevalue="" label="Sort by name" help="Checked: sort by name; Unchecked: sort by coordinate"/> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
137 </when> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
138 --> |
0 | 139 </conditional> |
140 </inputs> | |
141 <outputs> | |
3
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
142 <data format="txt" name="out_file1"> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
143 <change_format> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
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diff
changeset
|
144 <when input="analysis_type.format_type.format_type_selector" value="bed" format="bed" /> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
145 <when input="analysis_type.format_type.format_type_selector" value="fasta" format="fasta" /> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
146 <when input="analysis_type.format_type.format_type_selector" value="fastq" format="fastq" /> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
147 <when input="analysis_type.format_type.format_type_selector" value="sam" format="sam" /> |
04866f817daa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
2
diff
changeset
|
148 <when input="analysis_type.format_type.format_type_selector" value="pileup" format="pileup" /> |
7
ddb22028b552
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools commit 862f05b5053f55def8007194a702019418697cb5
iuc
parents:
6
diff
changeset
|
149 <when input="analysis_type.format_type.format_type_selector" value="json" format="json" /> |
4
4d343c1f606b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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150 <when input="analysis_type.analysis_type_selector" value="count" format="tabular" /> |
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151 <when input="analysis_type.analysis_type_selector" value="coverage" format="tabular" /> |
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152 <when input="analysis_type.analysis_type_selector" value="merge" format="bam" /> |
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153 <when input="analysis_type.analysis_type_selector" value="random" format="bam" /> |
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154 <when input="analysis_type.analysis_type_selector" value="revert" format="bam" /> |
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155 <when input="analysis_type.analysis_type_selector" value="sort" format="bam" /> |
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156 </change_format> |
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157 </data> |
0 | 158 </outputs> |
159 <tests> | |
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160 <test> |
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161 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> |
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162 <param name="analysis_type_selector" value="convert"/> |
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163 <param name="format_type_selector" value="pileup"/> |
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164 <param name="reference_source_selector" value="history" /> |
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165 <param name="mapqual" value="true" /> |
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166 <param name="ref_file" ftype="fasta" value="bamtools-fasta.fa"/> |
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167 <output name="out_file1" file="bamtools-convert-pileup.pu" /> |
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168 </test> |
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169 <test> |
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170 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> |
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171 <param name="analysis_type_selector" value="count"/> |
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172 <output name="out_file1" file="bamtools-count.tab" /> |
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173 </test> |
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174 <test> |
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175 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> |
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176 <param name="analysis_type_selector" value="coverage"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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177 <output name="out_file1" file="bamtools-coverage.tab" /> |
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178 </test> |
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179 <test> |
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180 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> |
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181 <param name="analysis_type_selector" value="header"/> |
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182 <output name="out_file1" file="bamtools-header.txt" /> |
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183 </test> |
0 | 184 </tests> |
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185 <help> |
0 | 186 |
187 **What is does** | |
188 | |
189 BAMTools is a collection of utilities for manipulation on BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools). | |
190 This Galaxy implementation of BAMTools utilities includes seven utilities - Convert, Count, Coverage, Header, Merge, Random, and Revert - decsribed in detail below. | |
191 | |
192 ----- | |
193 | |
194 **Convert** | |
195 | |
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196 Converts BAM dataset(s) into BED, FASTA, FASTQ, JSON, Pileup, SAM, or YAML formats. Note that the conversion to the pileup format requires providing a reference sequence either cached on this Galaxy instance, or provided by you as a FASTA dataset from History. |
0 | 197 |
198 ----- | |
199 | |
200 **Count** | |
201 | |
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202 Counts the number of alignments in a BAM dataset(s). |
0 | 203 |
204 ----- | |
205 | |
206 **Coverage** | |
207 | |
208 Prints per-base coverage for a BAM dataset. | |
209 | |
210 ----- | |
211 | |
212 **Header** | |
213 | |
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214 Prints the header of a BAM dataset. |
0 | 215 |
216 ------ | |
217 | |
218 **Merge** | |
219 | |
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220 Merges multiple BAM datasets into a single one. |
0 | 221 |
222 ------ | |
223 | |
224 **Random** | |
225 | |
226 Grabs a specified number of random lines from BAM dataset(s). | |
227 | |
228 ------ | |
229 | |
230 **Revert** | |
231 | |
232 Removes duplicate marks and restores original (non-recalibrated) base qualities. | |
233 | |
234 ----- | |
235 | |
236 .. class:: infomark | |
237 | |
238 **More information** | |
239 | |
240 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki | |
241 | |
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242 </help> |
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243 <citations> |
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244 <citation type="doi">10.1093/bioinformatics/btr174</citation> |
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245 </citations> |
0 | 246 </tool> |