Mercurial > repos > iuc > coverm_contig

annotate coverm_contig.xml @ 3:c2a5823e4763 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
author iuc
date Wed, 26 Jul 2023 07:35:24 +0000
parents f8cb3f0a19fa
children 1dcea261abbe
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688a777e1b19 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2388df7187533fb66b7729730340d2eb7b93c112
iuc
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1 <tool id="coverm_contig" name="CoverM contig" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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2 <description>Calculate read coverage per contig</description>
0
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3 <macros>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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4 <import>macros.xml</import>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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5 </macros>
3
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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6 <expand macro="bio_tools"/>
0
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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7 <expand macro="requirements"/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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8 <command><![CDATA[
3
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iuc
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9 #import re
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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10 #import os
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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11
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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12 #set $single_fp = []
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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13 #set $fw_fp = []
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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14 #set $rv_fp = []
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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15 #set $interl_fp = []
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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16 #set $ref_fp = []
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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17 #set $bam_fp = []
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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18
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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19 mkdir 'single/' &&
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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20 mkdir 'fw/' &&
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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21 mkdir 'rv/' &&
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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22 mkdir 'interl/' &&
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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23 mkdir 'ref/' &&
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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24 mkdir 'bam/' &&
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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25
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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26 #if $mapped.mapped == 'mapped'
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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27 @BAMS@
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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28 #else
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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29 #if $mapped.mode.mode == 'individual'
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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30 @INDIVIDUAL_ASSEMBLY_READS@
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iuc
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31 #set $ref = $mapped.mode.reference
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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32 @INDIVIDUAL_ASSEMBLY_REF@
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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33 #else
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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34 @CO_ASSEMBLY_ALL_READS@
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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35 #set $refs = $mapped.mode.reference
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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36 @CO_ASSEMBLY_REF@
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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37 #end if
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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38 #end if
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39
3
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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40 coverm
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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41 contig
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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42 #if $mapped.mapped == 'mapped'
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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43 -b
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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44 #for $bam in $bam_fp
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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45 '$bam'
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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46 #end for
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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47 $mapped.sharded
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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48 #else
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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49 #if $fw_fp
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50 -1
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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51 #for $read in $fw_fp
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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52 '$read'
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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53 #end for
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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54 -2
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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55 #for $read in $rv_fp
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56 '$read'
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57 #end for
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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58 #else if $single_fp
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59 --single
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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60 #for $read in $single_fp
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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61 '$read'
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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62 #end for
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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63 #else if $interl_fp
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64 --interleaved
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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65 #for $read in $interl_fp
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66 '$read'
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67 #end for
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68 #end if
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69 --reference
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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70 #for $ref in $ref_fp
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71 '$ref'
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72 #end for
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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73 #if $mapped.mode.mode == 'co'
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74 $mapped.mode.sharded
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75 #end if
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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76 --mapper '$mapped.mapper'
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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77 #end if
0
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78
3
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79 --min-read-aligned-length $alignment.min_read_aligned_length
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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80 --min-read-percent-identity $alignment.min_read_percent_identity
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81 --min-read-aligned-percent $alignment.min_read_aligned_percent
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82 $alignment.proper_pairs_only.proper_pairs_only
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83 #if $alignment.proper_pairs_only.proper_pairs_only != ''
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84 --min-read-aligned-length-pair $alignment.proper_pairs_only.min_read_aligned_length_pair
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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85 --min-read-percent-identity-pair $alignment.proper_pairs_only.min_read_percent_identity_pair
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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86 --min-read-aligned-percent-pair $alignment.proper_pairs_only.min_read_aligned_percent_pair
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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87 #end if
0
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88
3
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89 --methods
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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90 #for method in $cov.methods
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91 '$method'
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92 #end for
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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93 --min-covered-fraction $cov.min_covered_fraction
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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94 --contig-end-exclusion $cov.contig_end_exclusion
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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95 --trim-min $cov.trim_min
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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96 --trim-max $cov.trim_max
0
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97
3
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98 --output-format '$output_format'
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99 --output-file '$output'
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100 --threads \${GALAXY_SLOTS:-1}
0
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101 ]]></command>
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102 <inputs>
3
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103 <conditional name="mapped">
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104 <expand macro="mapped"/>
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105 <when value="mapped">
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106 <expand macro="mapped_params"/>
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107 </when>
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108 <when value="not-mapped">
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109 <conditional name="mode">
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110 <expand macro="assembly_mode"/>
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111 <when value="individual">
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112 <expand macro="individual_assembly_reads"/>
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113 <expand macro="individual_assembly_reference"/>
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114 </when>
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115 <when value="co">
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116 <expand macro="co_assembly_reads"/>
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117 <repeat name="extra_reads" title="Additional reads">
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118 <expand macro="co_assembly_reads"/>
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119 </repeat>
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120 <expand macro="co_assembly_reference"/>
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121 </when>
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122 </conditional>
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123 <expand macro="mapping"/>
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124 </when>
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125 </conditional>
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126 <expand macro="alignment"/>
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127 <section name="cov" title="Coverage calculation options" expanded="false">
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128 <param argument="--methods" type="select" multiple="true" label="Method(s) for calculating coverage">
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129 <option value="mean" selected="true">mean: Average number of aligned reads overlapping each position on the contig</option>
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130 <expand macro="cov_method_options"/>
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131 </param>
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132 <expand macro="coverage_params"/>
0
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133 </section>
3
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134 <expand macro="output_format"/>
0
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135 </inputs>
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136 <outputs>
3
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137 <data name="output" format="tabular"/>
0
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138 </outputs>
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139 <tests>
3
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140 <test expect_num_outputs="1">
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141 <conditional name="mapped">
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142 <param name="mapped" value="not-mapped" />
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143 <conditional name="mode">
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144 <param name="mode" value="co"/>
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145 <conditional name="read_type">
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146 <param name="type" value="paired_collection"/>
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147 <param name="paired_reads">
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148 <collection type="list:paired">
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149 <element name="reads_for_seq1_and_seq2">
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150 <collection type="paired">
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151 <element name="forward" value="reads_for_seq1_and_seq2.1.fq.gz" ftype="fastqsanger.gz"/>
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152 <element name="reverse" value="reads_for_seq1_and_seq2.2.fq.gz" ftype="fastqsanger.gz"/>
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153 </collection>
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154 </element>
0
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155 </collection>
3
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156 </param>
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157 </conditional>
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158 <param name="reference" value="7seqs.fna" />
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159 <param name="sharded" value="" />
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160 </conditional>
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161 </conditional>
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162 <section name="alignment">
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163 <param name="min_read_aligned_length" value="0" />
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164 <param name="min_read_percent_identity" value="0" />
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165 <param name="min_read_aligned_percent" value="0" />
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166 <conditional name="proper_pairs_only">
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167 <param name="proper_pairs_only" value=""/>
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168 </conditional>
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169 <param name="exclude_supplementary" value=""/>
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170 </section>
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171 <section name="cov">
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172 <param name="methods" value="mean"/>
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173 <param name="trim_min" value="5"/>
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174 <param name="trim_max" value="95"/>
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175 <param name="min_covered_fraction" value="10"/>
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176 <param name="contig_end_exclusion" value="75"/>
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177 </section>
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178 <param name="output_format" value="dense"/>
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179 <output name="output" ftype="tabular">
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180 <assert_contents>
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181 <has_text text="Contig"/>
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182 <has_text text="Mean"/>
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183 <has_text text="7seqs.fna"/>
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184 <has_text text="genome1~random_sequence_length_11000"/>
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185 <has_text text="genome2~seq1"/>
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186 </assert_contents>
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187 </output>
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188 </test>
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189 <test expect_num_outputs="1">
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190 <conditional name="mapped">
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191 <param name="mapped" value="not-mapped" />
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192 <conditional name="mode">
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193 <param name="mode" value="individual"/>
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194 <conditional name="read_type">
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195 <param name="type" value="paired"/>
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196 <param name="read1" value="reads_for_seq1_and_seq2.1.fq.gz" ftype="fastqsanger.gz"/>
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197 <param name="read2" value="reads_for_seq1_and_seq2.2.fq.gz" ftype="fastqsanger.gz"/>
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198 </conditional>
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199 <param name="reference" value="7seqs.fna" />
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200 <param name="sharded" value="" />
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201 </conditional>
0
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202 </conditional>
3
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203 <section name="alignment">
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204 <param name="min_read_aligned_length" value="0" />
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205 <param name="min_read_percent_identity" value="0" />
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206 <param name="min_read_aligned_percent" value="0" />
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207 <conditional name="proper_pairs_only">
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208 <param name="proper_pairs_only" value=""/>
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209 </conditional>
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210 <param name="exclude_supplementary" value=""/>
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211 </section>
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212 <section name="cov">
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213 <param name="methods" value="mean"/>
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214 <param name="trim_min" value="5"/>
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215 <param name="trim_max" value="95"/>
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216 <param name="min_covered_fraction" value="10"/>
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217 <param name="contig_end_exclusion" value="75"/>
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218 </section>
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219 <param name="output_format" value="dense"/>
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iuc
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220 <output name="output" ftype="tabular">
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221 <assert_contents>
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222 <has_text text="Contig"/>
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223 <has_text text="Mean"/>
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224 <has_text text="7seqs.fna"/>
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225 <has_text text="genome1~random_sequence_length_11000"/>
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226 <has_text text="genome2~seq1"/>
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227 </assert_contents>
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228 </output>
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229 </test>
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230 <test expect_num_outputs="1">
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231 <conditional name="mapped">
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232 <param name="mapped" value="not-mapped" />
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233 <conditional name="mode">
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234 <param name="mode" value="co"/>
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235 <conditional name="read_type">
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236 <param name="type" value="single"/>
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237 <param name="single" value="bad_reads.interleaved.fq"/>
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238 </conditional>
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239 <param name="reference" value="2seqs.fasta" />
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240 <param name="sharded" value="" />
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241 </conditional>
0
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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242 </conditional>
3
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243 <section name="alignment">
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244 <param name="min_read_aligned_length" value="0" />
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245 <param name="min_read_percent_identity" value="0" />
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246 <param name="min_read_aligned_percent" value="0" />
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247 <conditional name="proper_pairs_only">
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248 <param name="proper_pairs_only" value=""/>
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249 </conditional>
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250 <param name="exclude_supplementary" value=""/>
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251 </section>
0
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252 <section name="cov">
3
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253 <param name="methods" value="mean"/>
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254 <param name="trim_min" value="5"/>
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255 <param name="trim_max" value="95"/>
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256 <param name="min_covered_fraction" value="10"/>
0
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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257 <param name="contig_end_exclusion" value="0"/>
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258 </section>
3
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259 <param name="output_format" value="sparse"/>
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260 <output name="output" ftype="tabular">
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261 <assert_contents>
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262 <has_text text="Contig"/>
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263 <has_text text="Mean"/>
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264 <has_text text="Sample"/>
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265 <has_text text="2seqs.fasta_0/bad_reads.interleaved.fq_single_0"/>
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266 <has_text text="seq2"/>
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267 </assert_contents>
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268 </output>
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269 </test>
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270 <test expect_num_outputs="1">
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271 <conditional name="mapped">
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272 <param name="mapped" value="not-mapped" />
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273 <conditional name="mode">
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iuc
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274 <param name="mode" value="co"/>
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275 <conditional name="read_type">
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276 <param name="type" value="interleaved"/>
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277 <param name="interleaved" value="bad_reads.all.interleaved.fa"/>
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278 </conditional>
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279 <param name="reference" value="2seqs.fasta" />
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280 <param name="sharded" value="" />
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281 </conditional>
0
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282 </conditional>
3
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283 <section name="alignment">
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284 <param name="min_read_aligned_length" value="0" />
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285 <param name="min_read_percent_identity" value="0" />
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286 <param name="min_read_aligned_percent" value="0" />
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287 <conditional name="proper_pairs_only">
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288 <param name="proper_pairs_only" value=""/>
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289 </conditional>
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290 <param name="exclude_supplementary" value=""/>
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291 </section>
0
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292 <section name="cov">
3
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293 <param name="methods" value="mean"/>
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294 <param name="trim_min" value="5"/>
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295 <param name="trim_max" value="95"/>
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296 <param name="min_covered_fraction" value="10"/>
0
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297 <param name="contig_end_exclusion" value="0"/>
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298 </section>
3
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299 <param name="output_format" value="sparse"/>
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iuc
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300 <output name="output" ftype="tabular">
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301 <assert_contents>
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iuc
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302 <has_text text="Contig"/>
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iuc
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303 <has_text text="Mean"/>
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iuc
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304 <has_text text="Sample"/>
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iuc
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305 <has_text text="2seqs.fasta_0/bad_reads.all.interleaved.fa_interleaved_0"/>
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iuc
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306 <has_text text="seq1"/>
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iuc
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307 <has_text text="seq2"/>
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308 </assert_contents>
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309 </output>
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310 </test>
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311 <test expect_num_outputs="1">
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312 <conditional name="mapped">
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313 <param name="mapped" value="not-mapped" />
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iuc
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314 <conditional name="mode">
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iuc
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315 <param name="mode" value="co"/>
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iuc
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316 <conditional name="read_type">
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iuc
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317 <param name="type" value="paired"/>
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318 <param name="read1" value="reads_for_seq1_and_seq2.1.fq.gz"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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319 <param name="read2" value="reads_for_seq1_and_seq2.2.fq.gz"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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320 </conditional>
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iuc
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321 <repeat name="extra_reads">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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322 <conditional name="read_type">
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iuc
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323 <param name="type" value="paired_collection"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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324 <param name="paired_reads">
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iuc
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325 <collection type="list:paired">
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iuc
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diff changeset
326 <element name="reads_for_seq1_and_seq2">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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327 <collection type="paired">
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328 <element name="forward" value="reads_for_seq1_and_seq2.1.fq.gz" ftype="fastqsanger.gz"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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329 <element name="reverse" value="reads_for_seq1_and_seq2.2.fq.gz" ftype="fastqsanger.gz"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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330 </collection>
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331 </element>
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332 </collection>
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333 </param>
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334 </conditional>
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335 </repeat>
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336 <param name="reference" value="2seqs.fasta" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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337 <param name="sharded" value="" />
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338 </conditional>
0
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339 </conditional>
3
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340 <section name="alignment">
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iuc
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341 <param name="min_read_aligned_length" value="0" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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342 <param name="min_read_percent_identity" value="0.95" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
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343 <param name="min_read_aligned_percent" value="0" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
344 <conditional name="proper_pairs_only">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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345 <param name="proper_pairs-only" value=""/>
0
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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346 </conditional>
3
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347 <param name="exclude_supplementary" value=""/>
0
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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348 </section>
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349 <section name="cov">
3
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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parents: 2
diff changeset
350 <param name="methods" value="mean"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
351 <param name="trim_min" value="5"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
352 <param name="trim_max" value="95"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
353 <param name="min_covered_fraction" value="10"/>
0
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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354 <param name="contig_end_exclusion" value="0"/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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355 </section>
3
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iuc
parents: 2
diff changeset
356 <param name="output_format" value="sparse"/>
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iuc
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diff changeset
357 <output name="output" ftype="tabular">
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358 <assert_contents>
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iuc
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diff changeset
359 <has_text text="Contig"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
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360 <has_text text="Mean"/>
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iuc
parents: 2
diff changeset
361 <has_text text="Sample"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
362 <has_text text="2seqs.fasta_0/reads_for_seq1_and_seq2.1.fq.gz_paired_0"/>
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iuc
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diff changeset
363 <has_text text="2seqs.fasta_0/reads_for_seq1_and_seq2_paired_collection_00"/>
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iuc
parents: 2
diff changeset
364 <has_text text="seq1"/>
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iuc
parents: 2
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365 <has_text text="seq2"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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366 </assert_contents>
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iuc
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367 </output>
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iuc
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368 </test>
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iuc
parents: 2
diff changeset
369 <test expect_num_outputs="1">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
370 <conditional name="mapped">
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iuc
parents: 2
diff changeset
371 <param name="mapped" value="mapped" />
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iuc
parents: 2
diff changeset
372 <conditional name="mode">
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iuc
parents: 2
diff changeset
373 <param name="mode" value="co"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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diff changeset
374 <param name="bam_files" value="tpm_test.bam"/>
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iuc
parents: 2
diff changeset
375 <param name="sharded" value="" />
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iuc
parents: 2
diff changeset
376 </conditional>
0
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iuc
parents:
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377 </conditional>
3
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iuc
parents: 2
diff changeset
378 <section name="alignment">
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iuc
parents: 2
diff changeset
379 <param name="min_read_aligned_length" value="0" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
380 <param name="min_read_percent_identity" value="0.95" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
381 <param name="min_read_aligned_percent" value="0" />
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382 <conditional name="proper_pairs_only">
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383 <param name="proper_pairs-only" value=""/>
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384 </conditional>
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385 <param name="exclude_supplementary" value=""/>
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386 </section>
0
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387 <section name="cov">
3
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388 <param name="methods" value="mean,tpm"/>
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389 <param name="trim_min" value="5"/>
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390 <param name="trim_max" value="95"/>
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391 <param name="min_covered_fraction" value="10"/>
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392 <param name="contig_end_exclusion" value="75"/>
0
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393 </section>
3
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394 <param name="output_format" value="sparse"/>
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395 <output name="output" ftype="tabular">
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396 <assert_contents>
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397 <has_text text="Contig"/>
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398 <has_text text="Mean"/>
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399 <has_text text="Sample"/>
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400 <has_text text="TPM"/>
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401 <has_text text="tpm_test"/>
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402 <has_text text="genome1~random_sequence_length_11000"/>
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403 <has_text text="genome2~seq1"/>
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404 <has_text text="genome3~random_sequence_length_11001"/>
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405 </assert_contents>
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406 </output>
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407 </test>
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408 <test expect_num_outputs="1">
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409 <conditional name="mapped">
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410 <param name="mapped" value="mapped" />
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411 <conditional name="mode">
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412 <param name="mode" value="co"/>
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413 <param name="bam_files" value="tpm_test.bam"/>
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414 <param name="sharded" value="" />
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415 </conditional>
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416 </conditional>
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417 <section name="alignment">
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418 <param name="min_read_aligned_length" value="0" />
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419 <param name="min_read_percent_identity" value="0.95" />
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420 <param name="min_read_aligned_percent" value="0" />
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421 <conditional name="proper_pairs_only">
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422 <param name="proper_pairs-only" value=""/>
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423 </conditional>
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424 <param name="exclude_supplementary" value=""/>
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425 </section>
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426 <section name="cov">
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427 <param name="methods" value="mean,tpm"/>
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428 <param name="trim_min" value="5"/>
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429 <param name="trim_max" value="95"/>
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430 <param name="min_covered_fraction" value="10"/>
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431 <param name="contig_end_exclusion" value="75"/>
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432 </section>
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433 <param name="output_format" value="sparse"/>
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434 <output name="output" ftype="tabular">
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435 <assert_contents>
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436 <has_text text="Contig"/>
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437 <has_text text="Mean"/>
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438 <has_text text="Sample"/>
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439 <has_text text="TPM"/>
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440 <has_text text="tpm_test"/>
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441 <has_text text="genome1~random_sequence_length_11000"/>
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442 <has_text text="genome2~seq1"/>
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443 <has_text text="genome3~random_sequence_length_11001"/>
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444 </assert_contents>
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445 </output>
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446 </test>
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447 </tests>
0
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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448 <help><![CDATA[
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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449 .. class:: infomark
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450
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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451 **Method for calculating coverage**
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452
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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453 Calculation of genome-wise coverage (genome mode) is similar to calculating contig-wise (contig mode) coverage, except that the unit of reporting is per-genome rather than per-contig. For calculation methods which exclude base positions based on their coverage, all positions from all contigs are considered together.
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454
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455 - Relative abundance: Percentage relative abundance of each genome, and the unmapped read percentage
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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456 - Mean: Average number of aligned reads overlapping each position on the genome
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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457 - Trimmed mean: Average number of aligned reads overlapping each position after removing the most deeply and shallowly covered positions.
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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458 - Covered fraction: Fraction of genome covered by 1 or more reads
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459 - Covered bases: Number of bases covered by 1 or more reads
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460 - Variance: Variance of coverage depths
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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461 - Length: Length of each genome in base pairs
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462 - Count: Number of reads aligned toq each genome. Note that a single read may be aligned to multiple genomes with supplementary alignments
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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463 - Reads per base: Number of reads aligned divided by the length of the genome
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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464 - MetaBAT: Reproduction of the `MetaBAT <https://bitbucket.org/berkeleylab/metabat>`_ tool output
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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465 - Coverage histogram: Histogram of coverage depths
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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466 - RPKM: Reads mapped per kilobase of genome, per million mapped reads
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467 - TPM: Transcripts Per Million as described in `Li et al 2010 <https://doi.org/10.1093/bioinformatics/btp692>`_
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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468
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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469 ]]></help>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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470 <expand macro="citation"/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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471 </tool>