Mercurial > repos > bgruening > nanopolish_variants

annotate macros.xml @ 8:bec636361cfd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
author bgruening
date Thu, 30 Nov 2023 17:57:59 +0000
parents 63af3144371a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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1 <macros>
8
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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2 <token name="@VERSION@">0.14.0</token>
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <token name="@PROFILE@">22.01</token>
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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5
0
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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6 <xml name="requirements">
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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7 <requirements>
5
63af3144371a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit dff183f4eb2d3df42917ec4fed0fbdb2ea11e19a"
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8 <requirement type="package" version="@VERSION@">nanopolish</requirement>
0
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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9 <yield/>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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10 </requirements>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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11 </xml>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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13 <!-- index outputs
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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14 <data name="output_index" format="nanopolish_index" from_work_dir="reads.fasta.index" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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15 <data name="output_index_fai" format="nanopolish_index_fai" from_work_dir="reads.fasta.index.fai" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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16 <data name="output_index_gzi" format="nanopolish_index_gzi" from_work_dir="reads.fasta.index.gzi" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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17 <data name="output_index_readdb" format="nanopolish_index_readdb" from_work_dir="reads.fasta.index.readdb" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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18 -->
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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19 <!-- <output name="output_index" file="reads.fasta.index" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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20 <output name="output_index_fai" file="reads.fasta.index.fai" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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21 <output name="output_index_gzi" file="reads.fasta.index.gzi" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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22 <output name="output_index_readdb" file="reads.fasta.index.readdb" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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23 -->
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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8
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bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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26 <token name="@PREPROCESS_INPUTS@"><![CDATA[
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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27 ln -s '$input_merged' reads.fasta &&
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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29 mkdir fast5_files &&
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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30 #if $input_reads_raw.extension == 'fast5':
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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31 ln -s '$input_reads_raw' fast5_files/read1.fast5 &&
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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33 #else if $input_reads_raw.extension == 'fast5.tar':
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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34 ln -s '$input_reads_raw' fast5_files.tar &&
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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35 tar -xf fast5_files.tar -C fast5_files &&
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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37 #else if $input_reads_raw.extension == 'fast5.tar.bz2':
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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38 ln -s '$input_reads_raw' fast5_files.tar.bz2 &&
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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39 tar -xjf fast5_files.tar.bz2 -C fast5_files &&
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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41 #else if $input_reads_raw.extension == 'fast5.tar.xz':
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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42 ln -s '$input_reads_raw' fast5_files.tar.xz &&
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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43 tar -xf fast5_files.tar.xz -C fast5_files &&
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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44
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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45 #else if $input_reads_raw.extension == 'fast5.tar.gz':
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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46 ln -s '$input_reads_raw' fast5_files.tar.gz &&
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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47 tar -xzf fast5_files.tar.gz -C fast5_files &&
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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48
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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49 #else:
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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50 echo 'Unsupported fast5 input type' &&
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51 exit 1 &&
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52
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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53 #end if
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54
bec636361cfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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55 nanopolish index
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56 -d fast5_files/
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57 #if $adv.input_seq_summary:
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58 -s '$adv.input_seq_summary'
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59 #end if
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60 reads.fasta &&
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61
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62 ln -s '$b' reads.bam &&
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63 ln -s '${b.metadata.bam_index}' reads.bam.bai &&
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64 #if $reference_source.reference_source_selector == 'history':
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65 ln -f -s '$reference_source.ref_file' genome.fa &&
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66 #else:
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67 ln -f -s '$reference_source.ref_file.fields.path' genome.fa &&
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68 #end if
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69 ]]></token>
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70
0
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71 <xml name="citations">
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72 <citations>
3
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
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73 <citation type="doi">10.1038/nmeth.3444</citation>
0
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74 <citation type="doi">10.1038/nmeth.4184</citation>
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75 <yield />
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76 </citations>
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77 </xml>
1
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78 </macros>