Mercurial > repos > devteam > samtools_sort
annotate macros.xml @ 3:e613c1ad4c4c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 64305ae905dc79e44b478203000add73598bcca1
author | iuc |
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date | Sat, 06 Apr 2019 06:37:47 -0400 |
parents | f56bdb93ae58 |
children | 6c2c1836728b |
rev | line source |
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0 | 1 <macros> |
2 <xml name="requirements"> | |
3 <requirements> | |
2
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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4 <requirement type="package" version="@TOOL_VERSION@">samtools</requirement> |
0 | 5 <yield/> |
6 </requirements> | |
7 </xml> | |
2
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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8 <token name="@TOOL_VERSION@">1.9</token> |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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9 <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token> |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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10 <token name="@PREPARE_IDX@"><![CDATA[ |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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11 ##prepare input and indices |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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12 ln -s '$input' infile && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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13 #if $input.is_of_type('bam'): |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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14 #if str( $input.metadata.bam_index ) != "None": |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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15 ln -s '${input.metadata.bam_index}' infile.bai && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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16 #else: |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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17 samtools index infile infile.bai && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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18 #end if |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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19 #elif $input.is_of_type('cram'): |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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changeset
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20 #if str( $input.metadata.cram_index ) != "None": |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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21 ln -s '${input.metadata.cram_index}' infile.crai && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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22 #else: |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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23 samtools index infile infile.crai && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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24 #end if |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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changeset
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25 #end if |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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26 ]]></token> |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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27 <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[ |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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changeset
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28 ##prepare input and indices |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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29 #for $i, $bam in enumerate( $input_bams ): |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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30 ln -s '$bam' '${i}' && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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changeset
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31 #if $bam.is_of_type('bam'): |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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changeset
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32 #if str( $bam.metadata.bam_index ) != "None": |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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33 ln -s '${bam.metadata.bam_index}' '${i}.bai' && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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34 #else: |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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35 samtools index '${i}' '${i}.bai' && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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36 #end if |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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37 #elif $bam.is_of_type('cram'): |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents:
1
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38 #if str( $bam.metadata.cram_index ) != "None": |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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39 ln -s '${bam.metadata.cram_index}' '${i}.crai' && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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40 #else: |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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41 samtools index '${i}' '${i}.crai' && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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42 #end if |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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43 #end if |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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44 #end for |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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45 ]]></token> |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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46 <token name="@PREPARE_FASTA_IDX@"><![CDATA[ |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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47 ##checks for reference data ($addref_cond.addref_select=="history" or =="cached") |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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48 ##and sets the -t/-T parameters accordingly: |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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49 ##- in case of history a symbolic link is used because samtools (view) will generate |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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50 ## the index which might not be possible in the directory containing the fasta file |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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51 ##- in case of cached the absolute path is used which allows to read the cram file |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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52 ## without specifying the reference |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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53 #if $addref_cond.addref_select == "history": |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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54 ln -s '${addref_cond.ref}' reference.fa && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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55 samtools faidx reference.fa && |
3
e613c1ad4c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 64305ae905dc79e44b478203000add73598bcca1
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56 #set reffa="reference.fa" |
2
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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57 #set reffai="reference.fa.fai" |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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58 #elif $addref_cond.addref_select == "cached": |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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59 #set reffa=str($addref_cond.ref.fields.path) |
3
e613c1ad4c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 64305ae905dc79e44b478203000add73598bcca1
iuc
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60 #set reffai=str($addref_cond.ref.fields.path)+".fai" |
2
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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61 #else |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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62 #set reffa=None |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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63 #set reffai=None |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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64 #end if |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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65 ]]></token> |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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66 <token name="@ADDTHREADS@"><![CDATA[ |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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67 ##compute the number of ADDITIONAL threads to be used by samtools (-@) |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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68 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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69 ]]></token> |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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70 <token name="@ADDMEMORY@"><![CDATA[ |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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71 ##compute the number of memory available to samtools sort (-m) |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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72 ##use only 75% of available: https://github.com/samtools/samtools/issues/831 |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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73 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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74 ((addmemory=addmemory*75/100)) && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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75 ]]></token> |
3
e613c1ad4c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 64305ae905dc79e44b478203000add73598bcca1
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76 <xml name="seed_input"> |
e613c1ad4c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 64305ae905dc79e44b478203000add73598bcca1
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77 <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> |
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78 </xml> |
2
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79 <xml name="flag_options"> |
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80 <option value="1">read is paired</option> |
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81 <option value="2">read is mapped in a proper pair</option> |
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82 <option value="4">read is unmapped</option> |
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83 <option value="8">mate is unmapped</option> |
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84 <option value="16">read reverse strand</option> |
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85 <option value="32">mate reverse strand</option> |
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86 <option value="64">read is the first in a pair</option> |
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87 <option value="128">read is the second in a pair</option> |
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88 <option value="256">alignment or read is not primary</option> |
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89 <option value="512">read fails platform/vendor quality checks</option> |
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90 <option value="1024">read is a PCR or optical duplicate</option> |
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91 <option value="2048">supplementary alignment</option> |
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92 </xml> |
3
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93 |
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94 <!-- region specification macros and tokens for tools that allow the specification |
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95 of region by bed file / space separated list of regions --> |
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96 <token name="@REGIONS_FILE@"><![CDATA[ |
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97 #if $cond_region.select_region == 'tab': |
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98 -t '$cond_region.targetregions' |
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99 #end if |
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100 ]]></token> |
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101 <token name="@REGIONS_MANUAL@"><![CDATA[ |
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102 #if $cond_region.select_region == 'text': |
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103 #for $i, $x in enumerate($cond_region.regions_repeat): |
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104 '${x.region}' |
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105 #end for |
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106 #end if |
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107 ]]></token> |
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108 <xml name="regions_macro"> |
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109 <conditional name="cond_region"> |
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110 <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)"> |
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111 <option value="no" selected="True">No</option> |
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112 <option value="text">Manualy specify regions</option> |
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113 <option value="tab">Regions from tabular file</option> |
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114 </param> |
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115 <when value="no"/> |
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116 <when value="text"> |
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117 <repeat name="regions_repeat" min="1" default="1" title="Regions"> |
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118 <param name="region" type="text" label="region" help="format chr:from-to"> |
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119 <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$</validator> |
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120 </param> |
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121 </repeat> |
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122 </when> |
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123 <when value="tab"> |
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124 <param name="targetregions" argument="-t/--target-regions" type="data" format="tabular" label="Target regions file" help="Do stats in these regions only. Tab-delimited file chr,from,to (1-based, inclusive)" /> |
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125 </when> |
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126 </conditional> |
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127 </xml> |
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128 |
0 | 129 <xml name="citations"> |
130 <citations> | |
131 <citation type="bibtex"> | |
132 @misc{SAM_def, | |
133 title={Definition of SAM/BAM format}, | |
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134 url = {https://samtools.github.io/hts-specs/},} |
0 | 135 </citation> |
136 <citation type="doi">10.1093/bioinformatics/btp352</citation> | |
137 <citation type="doi">10.1093/bioinformatics/btr076</citation> | |
138 <citation type="doi">10.1093/bioinformatics/btr509</citation> | |
139 <citation type="bibtex"> | |
140 @misc{Danecek_et_al, | |
141 Author={Danecek, P., Schiffels, S., Durbin, R.}, | |
142 title={Multiallelic calling model in bcftools (-m)}, | |
143 url = {http://samtools.github.io/bcftools/call-m.pdf},} | |
144 </citation> | |
145 <citation type="bibtex"> | |
146 @misc{Durbin_VCQC, | |
147 Author={Durbin, R.}, | |
148 title={Segregation based metric for variant call QC}, | |
149 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} | |
150 </citation> | |
151 <citation type="bibtex"> | |
152 @misc{Li_SamMath, | |
153 Author={Li, H.}, | |
154 title={Mathematical Notes on SAMtools Algorithms}, | |
155 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} | |
156 </citation> | |
157 <citation type="bibtex"> | |
158 @misc{SamTools_github, | |
159 title={SAMTools GitHub page}, | |
160 url = {https://github.com/samtools/samtools},} | |
161 </citation> | |
162 </citations> | |
163 </xml> | |
164 <xml name="version_command"> | |
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165 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command> |
0 | 166 </xml> |
167 <xml name="stdio"> | |
168 <stdio> | |
169 <exit_code range="1:" level="fatal" description="Error" /> | |
170 </stdio> | |
171 </xml> | |
172 </macros> |