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annotate moabs.xml @ 1:8c8cc81b34cd draft

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"planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit 6a45aa4c34b4f3b73ab0c6c3d9e7a315b62bf761"
author iuc
date Sat, 11 Apr 2020 04:14:34 -0400
parents 26d7ec4af119
children 214874e24cd6
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1
8c8cc81b34cd "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit 6a45aa4c34b4f3b73ab0c6c3d9e7a315b62bf761"
iuc
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1 <tool id="moabs" name="MOABS" profile="16.04" version="@VERSION@+galaxy1">
0
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2 <description>MOdel based Analysis of Bisulfite Sequencing data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code">
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8 <![CDATA[
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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9 #if str( $mcomp_advanced.doComp.compare_selector ) == "0":
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10 cp -f '$mcomp_advanced.doComp.compFile' comp.g1.vs.g2.txt &&
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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11 #end if
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12 moabs -v 1 --def MMAP.p="\${GALAXY_SLOTS:-4}" --def MCALL.p="\${GALAXY_SLOTS:-4}" --def MCOMP.p="\${GALAXY_SLOTS:-4}" --cf '$cfg_file' &&
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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13 #if "1" in $output_selector:
1
8c8cc81b34cd "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit 6a45aa4c34b4f3b73ab0c6c3d9e7a315b62bf761"
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14 cp -f dmc_M2_g1.G.bed_vs_g2.G.bed.txt '$output1' &&
0
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15 #end if
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16 #if "2" in $output_selector:
1
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17 cp -f dmr_M2_g1.G.bed_vs_g2.G.bed.txt '$output2' &&
8c8cc81b34cd "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit 6a45aa4c34b4f3b73ab0c6c3d9e7a315b62bf761"
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18 #end if
8c8cc81b34cd "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit 6a45aa4c34b4f3b73ab0c6c3d9e7a315b62bf761"
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19 #if "3" in $output_selector:
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20 cp -f comp.g1.vs.g2.txt '$output3' &&
0
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21 #end if
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22 echo Done
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23 ]]>
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24 </command>
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25 <configfiles>
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26 <configfile name="cfg_file">
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27 #if str( $reference_source.reference_source_selector ) == "history":
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28 #set $reference_fasta_filename = $reference_source.ref_file
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29 #else:
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30 #set $reference_fasta_filename = $reference_source.ref_file.fields.path
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31 #end if
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32 [INPUT]
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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33 #for $i, $s in enumerate( $g1_fastq )
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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34 #if str( $s.fastq_input.fastq_input_selector ) == "paired":
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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35 s1_r${i+1}_1='$s.fastq_input.fastq_input1'
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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36 s1_r${i+1}_2='$s.fastq_input.fastq_input2'
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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37 #elif str( $s.fastq_input.fastq_input_selector ) == "paired_collection":
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38 s1_r${i+1}_1='$s.fastq_input.fastq_input1.forward'
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39 s1_r${i+1}_2='$s.fastq_input.fastq_input1.reverse'
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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40 #else:
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41 s1_r${i+1}='$s.fastq_input.fastq_input1'
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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42 #end if
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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43 #end for
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44
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45 #for $i, $s in enumerate( $g2_fastq )
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46 #if str( $s.fastq_input.fastq_input_selector ) == "paired":
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47 s2_r${i+1}_1='$s.fastq_input.fastq_input1'
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48 s2_r${i+1}_2='$s.fastq_input.fastq_input2'
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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49 #elif str( $s.fastq_input.fastq_input_selector ) == "paired_collection":
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50 s2_r${i+1}_1='$s.fastq_input.fastq_input1.forward'
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51 s2_r${i+1}_2='$s.fastq_input.fastq_input1.reverse'
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52 #else:
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53 s2_r${i+1}='$s.fastq_input.fastq_input1'
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54 #end if
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55 #end for
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56
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57 [TASK]
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58 Program=MMAP
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59 Label=g1,g2
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60 Parallel=NONE
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61
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62 [MMAP]
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63 Path=bsmap
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64 d='${reference_fasta_filename}'
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65 #if str( $bsmap_advanced.bsmap_mismatch.bsmap_mismatch_selector ) != "0":
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66 v=$bsmap_advanced.bsmap_mismatch.v
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67 #end if
1
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68 s=$bsmap_advanced.s
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69 w=$bsmap_advanced.w
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70 #if $bsmap_advanced.D:
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71 D=$bsmap_advanced.D
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72 #end if
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73 S=$bsmap_advanced.S
0
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74 n=$bsmap_advanced.n
1
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75 q=$bsmap_advanced.q
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76 z=$bsmap_advanced.z
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77 f=$bsmap_advanced.f
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78 #if $bsmap_advanced.A:
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79 A=$bsmap_advanced.A
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80 #end if
0
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81 r=$bsmap_advanced.r
1
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82 #if str( $bsmap_advanced.R ) == "1":
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83 R=''
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84 #end if
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85 #if str( $bsmap_advanced.u ) == "1":
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86 u=''
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87 #end if
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88 m=$bsmap_advanced.m
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89 x=$bsmap_advanced.x
0
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90
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91 [MCALL]
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92 Path=mcall
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93 r='${reference_fasta_filename}'
1
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94 cytosineMinScore=$mcall_advanced.cytosineMinScore
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95 nextBaseMinScore=$mcall_advanced.nextBaseMinScore
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96 qualityScoreBase=$mcall_advanced.qualityScoreBase
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97 trimWGBSEndRepairPE2Seq=$mcall_advanced.trimWGBSEndRepairPE2Seq
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98 trimWGBSEndRepairPE1Seq=$mcall_advanced.trimWGBSEndRepairPE1Seq
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99 processPEOverlapSeq=$mcall_advanced.processPEOverlapSeq
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100 trimRRBSEndRepairSeq=$mcall_advanced.trimRRBSEndRepairSeq
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101 minFragSize=$mcall_advanced.minFragSize
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102 minMMFragSize=$mcall_advanced.minMMFragSize
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103 reportCpX=$mcall_advanced.reportCpX
0
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104
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105 [MCOMP]
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106 Path=mcomp
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107 doComp=$mcomp_advanced.doComp.compare_selector
1
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108 d=$mcomp_advanced.d
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109 filterCredibleDif=$mcomp_advanced.filterCredibleDif
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110 pFetDmc=$mcomp_advanced.pFetDmc
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111 pFetDmr=$mcomp_advanced.pFetDmr
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112 minNominalDif=$mcomp_advanced.minNominalDif
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113 minCredibleDif=$mcomp_advanced.minCredibleDif
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114 minDmcsInDmr=$mcomp_advanced.minDmcsInDmr
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115 maxDistConsDmcs=$mcomp_advanced.maxDistConsDmcs
0
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116 </configfile>
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117 </configfiles>
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118
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119 <inputs>
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120 <conditional name="reference_source">
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121 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a cache FASTA?" help="Cached FASTA">
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122 <option value="cached">Use a cached genome FASTA</option>
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123 <option value="history">Use a genome FASTA from history</option>
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124 </param>
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125 <when value="cached">
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126 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
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127 <options from_data_table="all_fasta">
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128 <filter type="sort_by" column="2" />
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129 <validator type="no_options" message="No genome FASTA are available" />
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130 </options>
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131 </param>
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132 </when>
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133 <when value="history">
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134 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
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135 </when>
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136 </conditional>
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137 <repeat name="g1_fastq" title="Group1: fastq files" min="1">
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138 <conditional name="fastq_input">
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139 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
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140 <option value="single">Single</option>
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141 <option value="paired">Paired</option>
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142 <option value="paired_collection">Paired Collection</option>
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143 </param>
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144 <when value="paired">
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145 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/>
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146 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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147 </when>
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148 <when value="single">
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149 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with single reads"/>
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150 </when>
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151 <when value="paired_collection">
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152 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
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153 </when>
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154 </conditional>
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155 </repeat>
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156 <repeat name="g2_fastq" title="Group2: fastq files" min="1">
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157 <conditional name="fastq_input">
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158 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
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159 <option value="single">Single</option>
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160 <option value="paired">Paired</option>
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161 <option value="paired_collection">Paired Collection</option>
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162 </param>
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163 <when value="paired">
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164 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/>
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165 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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166 </when>
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167 <when value="single">
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168 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with single reads"/>
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169 </when>
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170 <when value="paired_collection">
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171 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
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172 </when>
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173 </conditional>
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174 </repeat>
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175 <section name="bsmap_advanced" title="Advanced options for BSMAP" expanded="False">
1
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176 <param argument="-s" type="integer" value="16" min="8" max="16" label="Seed size" help="The seed size for the HASH table. BSMAP implements a seeding algorithm by indexing reference for all possible k-mers, i.e. seeds. As for the seed size, i.e. the length of k-mers, 16 is suggested for the WGBS mode, and 12 is suggested for the RRBS mode. Min=8, max=16."/>
0
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177 <conditional name="bsmap_mismatch">
1
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178 <param name="bsmap_mismatch_selector" type="select" label="Set the mismatch rate or number?" help="When `Do not set` selected, BSMAP will allow a default suggested 8% mismatch rate. Otherwise, a customized mismatch can be controlled by specifying a mismatch rate or a mismatch number.">
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179 <option value="0" selected="true">Do not set</option>
0
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180 <option value="1">Set the mismatch rate</option>
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181 <option value="2">Set the mismatch number</option>
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182 </param>
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183 <when value="1">
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184 <param argument="-v" type="float" value="0.08" min="0" max="1" label="Mismatch rate" help="The mismatch rate w.r.t to the read length"/>
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185 </when>
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186 <when value="2">
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187 <param argument="-v" type="integer" value="3" min="0" label="Mismatch number" help="The maximum number of mismatches allowed on a read"/>
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188 </when>
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189 </conditional>
1
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190 <param argument="-w" type="integer" value="1000" min="0" max="1000" label="Maximum number of equal best hits to count" help="Maximum number of equal best hits to count. When multiple mapping occurs for a read, it should control the number of records to report. Default: 1000."/>
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191 <param argument="-D" type="text" label="Restriction enzyme digestion sites for RRBS mode" help="For RRBS data, this option activates RRBS mapping mode and set restriction enzyme digestion sites. Digestion position marked by '-', example: -D C-CGG for MspI digestion. default: none (WGBS mode).">
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192 <validator type="regex" message="Use A/T/C/G/- for restriction enzyme digestion sites">^[ATCG-]*$</validator>
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193 </param>
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194 <param argument="-S" type="integer" value="0" label="Random seed" help="Seed for random number generation used in selecting multiple hits. Other seed values generate pseudo random number based on read index number, to allow reproducible mapping results. Default=0 (get seed from system clock, mapping results not resproducible)."/>
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195 <param argument="-n" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Mapping to four strands?" help="Yes: map SE or PE reads to all 4 strands, i.e. ++, +-, -+, --; No: only map to 2 forward strands, i.e. BSW(++) and BSC(-+). For example, for a traditional library construction, two forward strands, ++ and -+, are sufficient for alignments. However, a Pico library construction needs all four-strand mappings."/>
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196 <param argument="-q" type="integer" value="0" min="0" max="40" label="Quality threshold in trimming" help="The quality threshold to trim read bases. To obtain an accurate mapping, low-quality bases should be skipped beforehand. Min=0, max=40. Default=0 (no trim)."/>
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197 <param argument="-z" type="select" label="Base quality" help="Base quality for sequencing reads, Illumina or Sanger.">
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198 <option value="33" selected="true">Sanger</option>
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199 <option value="64">Illumina</option>
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200 </param>
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201 <param argument="-f" type="integer" value="5" min="0" label="Maximum number of Ns in a read to filter out" help="To filter out low-quality reads containing >n Ns. Default=5."/>
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202 <param argument="-A" type="text" label="3' adapter sequence to trim" help="To trim 3' adapter sequence. Default: none (no trim).">
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203 <validator type="regex" message="Use A/T/C/G for adapter sequences, and the length should be greater equal to 12 bases.">^[ATCG]{12,}$|^$</validator>
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204 </param>
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205 <param argument="-r" type="select" label="How to report repeat hits" help="0=none(unique hit/pair); 1=random one; 2=all(slow). When input reads coverage is high, it is suggested to report only unique hits (r=0). For a low-depth library, a random one from multiple mappings (r=1), or all multiple mappings (r=2) can be specified to increase read coverage, yet be cautious about bias caused by ambiguous mappings.">
0
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206 <option value="0" selected="true">0</option>
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207 <option value="1">1</option>
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208 <option value="2">2</option>
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209 </param>
1
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210 <param argument="-R" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Print corresponding reference sequences?" help="Yes: print corresponding reference sequences in mapping records, a `RS:` tag will be added in record attributes; No: do not print reference sequences."/>
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211 <param argument="-u" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Report unmapped reads?" help="Yes: print unmapped reads; No: do not print unmapped reads."/>
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212 <param argument="-m" type="integer" value="28" min="0" label="Minimal insert size allowed in paired-end mapping" help="For paired-end reads, the minimal insert size allowed in two end mapping. Default=28."/>
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213 <param argument="-x" type="integer" value="1000" min="0" label="Maximal insert size allowed in paired-end mapping" help="For paired-end reads, the maximal insert size allowed in two end mapping. Default=1000."/>
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214 </section>
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215 <section name="mcall_advanced" title="Advanced options for MCALL" expanded="False">
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216 <param argument="--cytosineMinScore" type="integer" value="20" min="0" label="Threshold for cytosine quality score" help="Threshold for cytosine quality score. Discard the base if threshold is not reached. Default=20."/>
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217 <param argument="--nextBaseMinScore" type="integer" value="3" min="-1" label="Threshold for the next base quality score" help="Threshold for the next base quality score. Possible values: -1 makes the program not to check if next base matches reference; any positive integer or zero makes the program to check if next base matches reference and reaches this score threshold; default=3, i.e., better than 'B' or '#'."/>
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218 <param argument="--qualityScoreBase" type="select" label="Specify the quality score system" help="Sanger, Solexa, or Illumina. See wiki FASTQ_format for details. Default: auto-detection.">
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219 <option value="0" selected="true">Auto-detection</option>
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220 <option value="33">Sanger</option>
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221 <option value="59">Solexa</option>
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222 <option value="64">Illumina</option>
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223 </param>
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224 <param argument="--trimWGBSEndRepairPE2Seq" type="integer" value="3" min="0" label="Bases to trim end-repair sequences from +-/--" help="To trim end-repair sequence from begin of +-/-- reads from Pair End WGBS Sequencing. 0: no trim; n (positive integer): trim n bases from begin of +-/-- reads. Default: trim 3 bases."/>
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225 <param argument="--trimWGBSEndRepairPE1Seq" type="integer" value="3" min="0" label="Bases to trim end-repair sequences from ++/-+" help="To trim end-repair sequence from end of ++/-+ reads from Pair End WGBS Sequencing. 0: no trim; n (positive integer): trim n bases from end of ++/-+ reads. Default: trim 3 bases."/>
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226 <param argument="--processPEOverlapSeq" type="select" label="Count once or twice the overlap sequence of two pairs" help="Two ends of paired-end reads may be overlapped in mapping. The overlap sequencce will be counted once or twice for cytosine methylation measurements. Default: once.">
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227 <option value="1" selected="true">Once</option>
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228 <option value="0">Twice</option>
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229 </param>
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230 <param argument="--trimRRBSEndRepairSeq" type="select" label="How to trim end-repair sequence for RRBS reads?" help="To trim end-repair sequence for RRBS reads. 0: no trim; 2: trim the last CG at exactly end of ++/-+ reads and trim the first CG at exactly begin of +-/-- reads like the WGBS situation. Default=2.">
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231 <option value="2" selected="true">2</option>
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232 <option value="0">0</option>
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233 </param>
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234 <param argument="--minFragSize" type="integer" value="0" min="0" label="Minimal fragment size for properly mapped reads" help="To retain properly mapped and large enough fragment sizes. The 9th field in the BAM file is the fragment size of the mapping, and non-properly-paired read has 0 at the 9th field. This option is set to require properly paired and large enough fragment size. Default=0 for all records."/>
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235 <param argument="--minMMFragSize" type="integer" value="0" min="0" label="Minimal fragment size for multiply matched read" help="Same as --minFragSize but this option is only applicable to reads with flag 0x100 set as 1, i.e., reads multiply mapped. Default=0 for all records."/>
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236 <param argument="--reportCpX" type="select" label="Generates CpG/A/C/T methylation?" help="To generate methylation for CpG, or CpA/CpC/CpT. Default=CpG.">
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237 <option value="G" selected="true">CpG</option>
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238 <option value="C">CpC</option>
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239 <option value="A">CpA</option>
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240 <option value="T">CpT</option>
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241 </param>
0
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242 </section>
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243 <section name="mcomp_advanced" title="Advanced options for MCOMP" expanded="False">
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244 <conditional name="doComp">
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245 <param name="compare_selector" type="select" label="Run the comparison or not" help="Yes: compare; No: do not compare, using the comparison result by `-c`">
1
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246 <option value="1" selected="true">Yes</option>
0
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247 <option value="0">No</option>
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248 </param>
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249 <when value="0">
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250 <param argument="-c" name="compFile" type="data" format="txt" label="Input comparison results" help="Previously generated comparison file from history"/>
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251 </when>
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252 </conditional>
1
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253 <param argument="-d" type="integer" value="3" min="0" label="Minimum depth for a site coverage" help="If a site has depth less than `d`, this site is ignored for statistical tests. This option affects much of nominal ratios but none of credible ratios. This option may be reset during later DMC/DMR rescan to filter sites with depth less than `d`. Default=3."/>
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254 <param argument="--filterCredibleDif" type="float" value="-10" label="Minimum absolute credible methylation difference (CDIF)" help="If absolute value of CDIF for a site less than filterCredibleDif, this site is ignored for regional calculation. Use a small value, such as 0.01, to filter all sites with no difference; use 0.20 (for example) to select DMCs. Any negative number means no filter. Default=-10."/>
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255 <param argument="--pFetDmc" type="float" value="0.05" min="0" max="1" label="Cutoff of Pvalue from Fisher Exact Test for DMC scan" help="Cutoff of P value from Fisher Exact Test for DMC scan. Default=`0.05`."/>
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256 <param argument="--pFetDmr" type="float" value="0.05" min="0" max="1" label="Cutoff of Pvalue from Fisher Exact Test for DMR scan" help="Cutoff of P value from Fisher Exact Test for DMR scan. Default=`0.05`."/>
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257 <param argument="--minNominalDif" type="float" value="0.33333" min="0" max="1" label="Minimal nominal methylation difference for DMC and DMR calling" help="Minimal nominal methylation difference for DMC and DMR. Default=`0.3333`."/>
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258 <param argument="--minCredibleDif" type="float" value="0.2" min="0" max="1" label="Minimal credible methylation difference for DMC calling" help="Minimal CDIF for DMC calling. Default=`0.2`."/>
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259 <param argument="--minDmcsInDmr" type="integer" value="3" min="1" label="Minimum number of DMCs in a DMR" help="Minimum number of DMCs in a DMR. Default=3."/>
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260 <param argument="--maxDistConsDmcs" type="integer" value="300" min="1" label="Maximum distance between two consective DMCs for a DMR" help="Maximum distance between two consective DMCs for a DMR. Default=300."/>
0
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261 </section>
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262 <param name="output_selector" type="select" multiple="true" optional="true" label="Select output files" help="">
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263 <option value="1" selected="true">dmc_M2_g1.G.bed_vs_g2.G.bed.txt</option>
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264 <option value="2" selected="true">dmr_M2_g1.G.bed_vs_g2.G.bed.txt</option>
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265 <option value="3" selected="true">comp.g1.vs.g2.txt</option>
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266 <option value="4" selected="true">BAM files</option>
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267 <option value="5" selected="true">Methylation calling BED files</option>
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268 </param>
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269 </inputs>
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270 <outputs>
1
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271 <data name="output1" format="interval" label="${tool.name} on ${on_string} : dmc_M2_g1.G.bed_vs_g2.G.bed.txt">
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272 <filter> "1" in output_selector </filter>
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273 </data>
1
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274 <data name="output2" format="interval" label="${tool.name} on ${on_string} : dmr_M2_g1.G.bed_vs_g2.G.bed.txt">
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275 <filter> "2" in output_selector </filter>
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276 </data>
1
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277 <data name="output3" format="interval" label="${tool.name} on ${on_string} : comp.g1.vs.g2.txt">
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278 <filter> "3" in output_selector </filter>
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279 </data>
0
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280 <collection name="output_collection_bam" type="list" label="BAM files">
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281 <filter> "4" in output_selector </filter>
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282 <discover_datasets pattern="(?P&lt;designation&gt;.+\.bam$)" ext='bam'/>
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283 </collection>
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284 <collection name="output_collection_bed" type="list" label="Methylation calling BED files">
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285 <filter> "5" in output_selector </filter>
0
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286 <discover_datasets pattern="(?P&lt;designation&gt;g[12]\.G\.bed$)" ext='interval'/>
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287 </collection>
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288 </outputs>
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289 <tests>
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290 <test>
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291 <!-- test single-end reads -->
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292 <param name="reference_source_selector" value="history"/>
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293 <param name="ref_file" ftype="fasta" value="chr11.fa"/>
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294 <repeat name="g1_fastq">
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295 <conditional name="fastq_input">
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296 <param name="fastq_input_selector" value="single"/>
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297 <param name="fastq_input1" value="WTPE1.fastq.gz"/>
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298 </conditional>
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299 </repeat>
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300 <repeat name="g1_fastq">
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301 <conditional name="fastq_input">
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302 <param name="fastq_input_selector" value="single"/>
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303 <param name="fastq_input1" value="WTPE2.fastq.gz"/>
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304 </conditional>
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305 </repeat>
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306 <repeat name="g2_fastq">
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307 <conditional name="fastq_input">
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308 <param name="fastq_input_selector" value="single"/>
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309 <param name="fastq_input1" value="TKO2PE1.fastq.gz"/>
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310 </conditional>
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311 </repeat>
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312 <repeat name="g2_fastq">
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313 <conditional name="fastq_input">
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314 <param name="fastq_input_selector" value="single"/>
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315 <param name="fastq_input1" value="TKO2PE2.fastq.gz"/>
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316 </conditional>
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317 </repeat>
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318 <conditional name="doComp">
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319 <param name="compare_selector" value="0"/>
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320 <param name="compFile" value="SE_comp.g1.vs.g2.txt"/>
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321 </conditional>
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322 <!--
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323 <conditional name="doComp">
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324 <param name="compare_selector" value="1"/>
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325 </conditional>
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326 -->
1
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327 <param name="output_selector" value="1,2,3,4,5"/>
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328 <output name="output1" file="SE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/>
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329 <output name="output2" file="SE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/>
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330 <output name="output3" file="SE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/>
0
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331 <output_collection name="output_collection_bam" count="4">
1
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332 <element name="g1_r1.bam" file="SE_g1_r1.bam" ftype="bam" lines_diff="2"/>
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333 <element name="g1_r2.bam" file="SE_g1_r2.bam" ftype="bam" lines_diff="2"/>
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334 <element name="g2_r1.bam" file="SE_g2_r1.bam" ftype="bam" lines_diff="2"/>
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335 <element name="g2_r2.bam" file="SE_g2_r2.bam" ftype="bam" lines_diff="2"/>
0
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336 </output_collection>
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337 <output_collection name="output_collection_bed" count="2">
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338 <element name="g1.G.bed" file="SE_g1.G.bed" ftype="interval" lines_diff="1"/>
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339 <element name="g2.G.bed" file="SE_g2.G.bed" ftype="interval" lines_diff="1"/>
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340 </output_collection>
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341 </test>
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342 <test>
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343 <!-- test paired-end reads -->
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344 <param name="reference_source_selector" value="history"/>
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345 <param name="ref_file" ftype="fasta" value="seg.fa"/>
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346 <repeat name="g1_fastq">
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347 <conditional name="fastq_input">
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348 <param name="fastq_input_selector" value="paired"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
349 <param name="fastq_input1" value="6_all_1.fq.gz"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
350 <param name="fastq_input2" value="6_all_2.fq.gz"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
351 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
352 </repeat>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
353 <repeat name="g2_fastq">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
354 <conditional name="fastq_input">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
355 <param name="fastq_input_selector" value="paired"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
356 <param name="fastq_input1" value="8_all_1.fq.gz"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
357 <param name="fastq_input2" value="8_all_2.fq.gz"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
358 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
359 </repeat>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
360 <conditional name="doComp">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
361 <param name="compare_selector" value="0"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
362 <param name="compFile" value="PE_comp.g1.vs.g2.txt"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
363 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
364 <!--
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
365 <conditional name="doComp">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
366 <param name="compare_selector" value="1"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
367 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
368 -->
1
8c8cc81b34cd "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit 6a45aa4c34b4f3b73ab0c6c3d9e7a315b62bf761"
iuc
parents: 0
diff changeset
369 <param name="output_selector" value="1,2,3"/>
8c8cc81b34cd "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit 6a45aa4c34b4f3b73ab0c6c3d9e7a315b62bf761"
iuc
parents: 0
diff changeset
370 <output name="output1" file="PE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/>
8c8cc81b34cd "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit 6a45aa4c34b4f3b73ab0c6c3d9e7a315b62bf761"
iuc
parents: 0
diff changeset
371 <output name="output2" file="PE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/>
8c8cc81b34cd "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit 6a45aa4c34b4f3b73ab0c6c3d9e7a315b62bf761"
iuc
parents: 0
diff changeset
372 <output name="output3" file="PE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/>
0
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
373 </test>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
374 <test>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
375 <!-- test paired collection -->
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
376 <param name="reference_source_selector" value="history"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
377 <param name="ref_file" ftype="fasta" value="seg.fa"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
378 <repeat name="g1_fastq">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
379 <conditional name="fastq_input">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
380 <param name="fastq_input_selector" value="paired_collection"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
381 <param name="fastq_input1">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
382 <collection type="paired">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
383 <element name="forward" value="6_all_1.fq.gz" />
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
384 <element name="reverse" value="6_all_2.fq.gz" />
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
385 </collection>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
386 </param>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
387 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
388 </repeat>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
389 <repeat name="g2_fastq">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
390 <conditional name="fastq_input">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
391 <param name="fastq_input_selector" value="paired_collection"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
392 <param name="fastq_input1">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
393 <collection type="paired">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
394 <element name="forward" value="8_all_1.fq.gz" />
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
395 <element name="reverse" value="8_all_2.fq.gz" />
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
396 </collection>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
397 </param>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
398 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
399 </repeat>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
400 <conditional name="doComp">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
401 <param name="compare_selector" value="0"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
402 <param name="compFile" value="PE_comp.g1.vs.g2.txt"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
403 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
404 <!--
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
405 <conditional name="doComp">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
406 <param name="compare_selector" value="1"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
407 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
408 -->
1
8c8cc81b34cd "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit 6a45aa4c34b4f3b73ab0c6c3d9e7a315b62bf761"
iuc
parents: 0
diff changeset
409 <param name="output_selector" value="1,2,3"/>
8c8cc81b34cd "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit 6a45aa4c34b4f3b73ab0c6c3d9e7a315b62bf761"
iuc
parents: 0
diff changeset
410 <output name="output1" file="PE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/>
8c8cc81b34cd "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit 6a45aa4c34b4f3b73ab0c6c3d9e7a315b62bf761"
iuc
parents: 0
diff changeset
411 <output name="output2" file="PE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/>
8c8cc81b34cd "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit 6a45aa4c34b4f3b73ab0c6c3d9e7a315b62bf761"
iuc
parents: 0
diff changeset
412 <output name="output3" file="PE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/>
0
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
413 </test>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
414 <test>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
415 <!-- test data table reference -->
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
416 <param name="reference_source_selector" value="cached"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
417 <param name="ref_file" value="chr11"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
418 <repeat name="g1_fastq">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
419 <conditional name="fastq_input">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
420 <param name="fastq_input_selector" value="single"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
421 <param name="fastq_input1" value="WTPE1.fastq.gz"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
422 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
423 </repeat>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
424 <repeat name="g1_fastq">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
425 <conditional name="fastq_input">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
426 <param name="fastq_input_selector" value="single"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
427 <param name="fastq_input1" value="WTPE2.fastq.gz"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
428 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
429 </repeat>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
430 <repeat name="g2_fastq">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
431 <conditional name="fastq_input">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
432 <param name="fastq_input_selector" value="single"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
433 <param name="fastq_input1" value="TKO2PE1.fastq.gz"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
434 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
435 </repeat>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
436 <repeat name="g2_fastq">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
437 <conditional name="fastq_input">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
438 <param name="fastq_input_selector" value="single"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
439 <param name="fastq_input1" value="TKO2PE2.fastq.gz"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
440 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
441 </repeat>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
442 <conditional name="doComp">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
443 <param name="compare_selector" value="0"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
444 <param name="compFile" value="SE_comp.g1.vs.g2.txt"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
445 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
446 <!--
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447 <conditional name="doComp">
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448 <param name="compare_selector" value="1"/>
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449 </conditional>
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450 -->
1
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451 <param name="output_selector" value="1,2,3"/>
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452 <output name="output1" file="SE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/>
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453 <output name="output2" file="SE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/>
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454 <output name="output3" file="SE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/>
0
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455 </test>
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456 </tests>
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457 <help>
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458 <![CDATA[
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459 **MOABS: MOdel based Analysis of Bisulfite Sequencing data**
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460
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461 MOABS is a comprehensive, accurate and efficient solution for analysis of large
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462 scale base-resolution DNA methylation data, bisulfite sequencing or single
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463 molecule direct sequencing.
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464
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465 MOABS seamlessly integrates alignment, methylation calling, identification of
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466 hypomethylation for one sample and differential methylation for multiple
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467 samples, and other downstream analysis.
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468
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469 For more information, check https://github.com/sunnyisgalaxy/moabs.
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470
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471 -----
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472
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473 **Input files**
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474
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475 MOABS needs to input Bisulfite sequencing reads in two groups of interest, e.g.
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476 KO vs WT. Each group of reads may have combined sequencing library, i.e.
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477 single-end reads and/or paired-end reads. Multiple replicates can be specified in each group.
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478
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479 **Outputs**
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480
1
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481 Five output files can be selected to report, namely
0
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482
1
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483 1. **DMC site file** - the major DMC result file
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484 2. **DMR region file** - the major DMR result file
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485 3. **Comparison file between two groups** - the intermediate comparion result
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486 4. **BAM files** - intermediate BAM files
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487 5. **Methylation BED files** - intermediate methylation BED files
0
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488
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489 -----
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490
1
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491 MOABS detects differentially methylated cytosines (DMCs) and differentially
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492 methylated regions (DMRs) using the input BS-Seq reads. The output DMC and DMR
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493 file are tab-delimited text files (not strictly a BED format), representing
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494 DMCs and DMRs.
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495
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496 A DMC site file has 15 columns as below.
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497
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498 chrom<TAB>start<TAB>end<TAB>totalC_0<TAB>nominalRatio_0<TAB>ratioCI_0<TAB>totalC_1<TAB>nominalRatio_1<TAB>ratioCI_1<TAB>nominalDif_1-0<TAB>credibleDif_1-0<TAB>difCI_1-0<TAB>p_sim_1_v_0<TAB>p_fet_1_v_0<TAB>class
0
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499
1
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500 1. **chrom** - The chromosome of the CpG site.
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501 2. **start** - The start genomic locus of the CpG site.
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502 3. **end** - The end genomic locus of the CpG site.
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503 4. **totalC_0** - The total number of CpG read coverage in group 0.
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504 5. **nominalRatio_0** - The nominal methylation ratio of the CpG in group 0.
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505 6. **ratioCI_0** - The confidence interval (CI) of the nominal methylation ratio at the CpG site in group 0.
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506 7. **totalC_1** - The total number of CpG read coverage in group 1.
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507 8. **nominalRatio_1** - The nominal methylation ratio of the CpG in group 1.
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508 9. **ratioCI_1** - The confidence interval (CI) of the nominal methylation ratio at the CpG site in group 1.
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509 10. **nominalDif_1-0** - The nominal methylation difference between the group 1 and the group 0.
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510 11. **credibleDif_1-0** - The credible methylation difference (CDIF) between the group 1 and the group 0.
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511 12. **difCI_1-0** - The difference of ratio CIs between the group 1 and the group 0.
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512 13. **p_sim_1_v_0** - P-value according to the similarity probablities.
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513 14. **p_fet_1_v_0** - P-value according to the Fisher exact test.
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514 15. **class** - 5-state class labels by methylation differences and p-values.
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515
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516 For example, CpGs in the DMC file are recorded in the following format.
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517
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518 @DMCExample@
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519
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520 A DMR result file has 12 columns as below.
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521
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522 chrom<TAB>start<TAB>end<TAB>meanRatio_0<TAB>totalC_0<TAB>cSites_0<TAB>meanRatio_1<TAB>totalC_1<TAB>cSites_1<TAB>methDif_1-0<TAB>p_1_v_0<TAB>class_1_v_0
0
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523
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524 1. **chrom** - The chromosome of the region.
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525 2. **start** - The start genomic locus of the region.
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526 3. **end** - The end genomic locus of the region.
1
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527 4. **meanRatio_0** - Mean methylation ratio of the region in group 0.
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528 5. **totalC_0** - Total cytosine coverage of the region in group 0.
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529 6. **cSites_0** - The number of CpG sites of the region in group 0.
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530 7. **meanRatio_1** - Mean methylation ratio of the region in group 1.
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531 8. **totalC_1** - Total cytosine coverage of the region in group 1.
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532 9. **cSites_1** - The number of CpG sites of the region in group 1.
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533 10. **methDif_1-0** - Average methylation difference of the region between group 1 and group 0.
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534 11. **p_1_v_0** - P-value from Fisher exact test of the region between group 1 and group 0.
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535 12. **class_1_v_0** - 5-state class labels for the DMR.
0
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536
1
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537 For example, four DMRs are identified in the following format.
0
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538
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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539 @DMRExample@
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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540
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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541 -----
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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542
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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543 The intermediate comparison file summarizes methylation ratio comparison
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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544 results on CpG sites. It has 19 columns as below.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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545
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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546 1. **chrom** - The chromosome of the GpG site.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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547 2. **start** - The start position of the site.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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548 3. **end** - The end position of the site.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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549 4. **single** - The next two columns are attributes for the single position.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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550 5. **totalC_0** - Total number of Cs in the first group.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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551 6. **nominalRatio_0** - Nominal methylation ratio in the first group.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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552 7. **ratioCI_0** - The confidence interval of the methylation ratio in the first group.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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553 8. **single** - The next two columns are attributes for the single position.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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554 9. **totalC_1** - Total number of Cs in the second group.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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555 10. **nominalRatio_1** - Nominal methylation ratio in the second group.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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556 11. **ratioCI_1** - The confidence interval of the methylation ratio in the second group.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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557 12. **pair** - The next three columns are attributes for pairs of groups.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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558 13. **nominalDif_1-0** - Nominal difference of methylation ratio between group 1 and group 0.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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559 14. **credibleDif_1-0** - Credible methylation difference between group 1 and group 0.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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560 15. **difCI_1-0** - Difference of confidence intervals between group 1 and group 0.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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561 16. **p_sim** - The next column is the simulation p-value.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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562 17. **p_sim_1_v_0** - Simulation p-value between group 1 and group 0.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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563 18. **p_fet** - The next column is the FET p-value.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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564 19. **p_fet_1_v_0** - FET p-value between group 1 and group 0.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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565
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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566 The comparison result file can be reused for DMR calling.
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567
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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568 -----
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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569
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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570 BAM files are intermediate mapping results of input reads to the referene
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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571 genome. These BAM files can be reused in downstream methylation analysis.
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572
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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573 -----
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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574
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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575 Methylation calling BED files are intermediate methylation calling results of
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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576 Cs in two groups of input reads. These methyation calling results can be easily
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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577 reused in downstream DMR calling and visualization. The BED file has 15 columns
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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578 as below.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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579
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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580 1. **chrom** - The chromosome of the site.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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581 2. **start** - The start position of the site.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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582 3. **end** - The end position of the site.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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583 4. **ratio** - Methylation ratio in the site
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584 5. **totalC** - Total number of reads in current Cs.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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585 6. **methC** - Methylated Cs.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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586 7. **strand** - The strand information for prevous three columns.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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587 8. **next** - The next base.
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588 9. **Plus** - Next two columns are for forward strand.
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589 10. **totalC** - Total number of Cs.
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590 11. **methC** - Methylated Cs.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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591 12. **Minus** - Next two columns are for reverse strand.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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592 13. **totalC** - Total number of Cs.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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593 14. **methC** - Methylated Cs.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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594 15. **localSeq** - Local sequences.
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595
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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596 ]]>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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597 </help>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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598 <expand macro="citations"/>
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599 </tool>