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annotate moabs.xml @ 0:26d7ec4af119 draft

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"planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
author iuc
date Fri, 06 Sep 2019 09:54:27 -0400
parents
children 8c8cc81b34cd
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0
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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1 <tool id="moabs" name="MOABS" profile="16.04" version="@VERSION@">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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2 <description>MOdel based Analysis of Bisulfite Sequencing data</description>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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3 <macros>
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4 <import>macros.xml</import>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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5 </macros>
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6 <expand macro="requirements"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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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 $output_selector:
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14 cp -f dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr '$output1' &&
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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15 #end if
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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16 #if "2" in $output_selector:
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17 cp -f comp.g1.vs.g2.txt '$output2' &&
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18 #end if
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19 echo Done
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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20 ]]>
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21 </command>
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22 <configfiles>
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23 <configfile name="cfg_file">
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24 #if str( $reference_source.reference_source_selector ) == "history":
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25 #set $reference_fasta_filename = $reference_source.ref_file
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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26 #else:
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27 #set $reference_fasta_filename = $reference_source.ref_file.fields.path
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28 #end if
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29 [INPUT]
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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30 #for $i, $s in enumerate( $g1_fastq )
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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31 #if str( $s.fastq_input.fastq_input_selector ) == "paired":
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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32 s1_r${i+1}_1='$s.fastq_input.fastq_input1'
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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33 s1_r${i+1}_2='$s.fastq_input.fastq_input2'
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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34 #elif str( $s.fastq_input.fastq_input_selector ) == "paired_collection":
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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35 s1_r${i+1}_1='$s.fastq_input.fastq_input1.forward'
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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36 s1_r${i+1}_2='$s.fastq_input.fastq_input1.reverse'
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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37 #else:
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38 s1_r${i+1}='$s.fastq_input.fastq_input1'
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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39 #end if
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40 #end for
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41
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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42 #for $i, $s in enumerate( $g2_fastq )
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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43 #if str( $s.fastq_input.fastq_input_selector ) == "paired":
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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44 s2_r${i+1}_1='$s.fastq_input.fastq_input1'
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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45 s2_r${i+1}_2='$s.fastq_input.fastq_input2'
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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46 #elif str( $s.fastq_input.fastq_input_selector ) == "paired_collection":
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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47 s2_r${i+1}_1='$s.fastq_input.fastq_input1.forward'
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48 s2_r${i+1}_2='$s.fastq_input.fastq_input1.reverse'
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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49 #else:
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50 s2_r${i+1}='$s.fastq_input.fastq_input1'
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51 #end if
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52 #end for
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53
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54 [TASK]
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55 Program=MMAP
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56 Label=g1,g2
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57 Parallel=NONE
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58
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59 [MMAP]
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60 Path=bsmap
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61 d='${reference_fasta_filename}'
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62 #if str( $bsmap_advanced.bsmap_mismatch.bsmap_mismatch_selector ) != "0":
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63 v=$bsmap_advanced.bsmap_mismatch.v
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64 #end if
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65 n=$bsmap_advanced.n
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66 r=$bsmap_advanced.r
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67 R=''
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68
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69 [MCALL]
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70 Path=mcall
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71 r='${reference_fasta_filename}'
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72
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73 [MCOMP]
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74 Path=mcomp
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75 reference='${reference_fasta_filename}'
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76 doComp=$mcomp_advanced.doComp.compare_selector
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77 </configfile>
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78 </configfiles>
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79
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80 <inputs>
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81 <conditional name="reference_source">
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82 <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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83 <option value="cached">Use a cached genome FASTA</option>
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84 <option value="history">Use a genome FASTA from history</option>
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85 </param>
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86 <when value="cached">
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87 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
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88 <options from_data_table="all_fasta">
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89 <filter type="sort_by" column="2" />
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90 <validator type="no_options" message="No genome FASTA are available" />
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91 </options>
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92 </param>
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93 </when>
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94 <when value="history">
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95 <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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96 </when>
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97 </conditional>
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98 <repeat name="g1_fastq" title="Group1: fastq files" min="1">
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99 <conditional name="fastq_input">
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100 <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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101 <option value="single">Single</option>
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102 <option value="paired">Paired</option>
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103 <option value="paired_collection">Paired Collection</option>
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104 </param>
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105 <when value="paired">
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106 <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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107 <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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108 </when>
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109 <when value="single">
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110 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with single reads"/>
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111 </when>
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112 <when value="paired_collection">
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113 <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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114 </when>
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115 </conditional>
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116 </repeat>
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117 <repeat name="g2_fastq" title="Group2: fastq files" min="1">
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118 <conditional name="fastq_input">
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119 <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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120 <option value="single">Single</option>
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121 <option value="paired">Paired</option>
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122 <option value="paired_collection">Paired Collection</option>
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123 </param>
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124 <when value="paired">
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125 <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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126 <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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127 </when>
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128 <when value="single">
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129 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with single reads"/>
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130 </when>
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131 <when value="paired_collection">
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132 <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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133 </when>
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134 </conditional>
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135 </repeat>
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136 <section name="bsmap_advanced" title="Advanced options for BSMAP" expanded="False">
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137 <conditional name="bsmap_mismatch">
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138 <param name="bsmap_mismatch_selector" type="select" label="Set the mismatch rate or number?" help="">
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139 <option value="0">Do not set</option>
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140 <option value="1">Set the mismatch rate</option>
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141 <option value="2">Set the mismatch number</option>
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142 </param>
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143 <when value="1">
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144 <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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145 </when>
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146 <when value="2">
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147 <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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148 </when>
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149 </conditional>
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150 <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(-+)"/>
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151 <param argument="-r" type="select" label="How to report repeat hits" help="0=none(unique hit/pair); 1=random one; 2=all(slow)">
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152 <option value="0" selected="true">0</option>
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153 <option value="1">1</option>
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154 <option value="2">2</option>
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155 </param>
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156 </section>
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157 <section name="mcomp_advanced" title="Advanced options for MCOMP" expanded="False">
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158 <conditional name="doComp">
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159 <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`">
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160 <option value="1">Yes</option>
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161 <option value="0">No</option>
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162 </param>
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163 <when value="0">
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164 <param argument="-c" name="compFile" type="data" format="txt" label="Input comparison results" help="Previously generated comparison file from history"/>
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165 </when>
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166 </conditional>
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167 </section>
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168 <param name="output_selector" type="select" multiple="true" optional="true" label="Select output files" help="">
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169 <option value="1"> dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr </option>
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170 <option value="2"> comp.g1.vs.g2.txt </option>
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171 <option value="3"> BAM files </option>
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172 <option value="4"> Methylation calling BED files </option>
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173 </param>
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174 </inputs>
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175 <outputs>
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176 <data name="output1" format="interval" label="${tool.name} on ${on_string} : dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr">
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177 <filter> "1" in output_selector </filter>
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178 </data>
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179 <data name="output2" format="interval" label="${tool.name} on ${on_string} : comp.g1.vs.g2.txt">
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180 <filter> "2" in output_selector </filter>
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181 </data>
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182 <collection name="output_collection_bam" type="list" label="BAM files">
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183 <filter> "3" in output_selector </filter>
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184 <discover_datasets pattern="(?P&lt;designation&gt;.+\.bam$)" ext='bam'/>
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185 </collection>
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186 <collection name="output_collection_bed" type="list" label="Methylation calling BED files">
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187 <filter> "4" in output_selector </filter>
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188 <discover_datasets pattern="(?P&lt;designation&gt;g[12]\.G\.bed$)" ext='interval'/>
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189 </collection>
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190 </outputs>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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191 <tests>
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192 <test>
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diff changeset
193 <!-- test single-end reads -->
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194 <param name="reference_source_selector" value="history"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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195 <param name="ref_file" ftype="fasta" value="chr11.fa"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
196 <repeat name="g1_fastq">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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diff changeset
197 <conditional name="fastq_input">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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198 <param name="fastq_input_selector" value="single"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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199 <param name="fastq_input1" value="WTPE1.fastq.gz"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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200 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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201 </repeat>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
202 <repeat name="g1_fastq">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
203 <conditional name="fastq_input">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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204 <param name="fastq_input_selector" value="single"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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diff changeset
205 <param name="fastq_input1" value="WTPE2.fastq.gz"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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206 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
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207 </repeat>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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diff changeset
208 <repeat name="g2_fastq">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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209 <conditional name="fastq_input">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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210 <param name="fastq_input_selector" value="single"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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diff changeset
211 <param name="fastq_input1" value="TKO2PE1.fastq.gz"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
212 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
213 </repeat>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
214 <repeat name="g2_fastq">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
215 <conditional name="fastq_input">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
216 <param name="fastq_input_selector" value="single"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
217 <param name="fastq_input1" value="TKO2PE2.fastq.gz"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
218 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
219 </repeat>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
220 <conditional name="doComp">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
221 <param name="compare_selector" value="0"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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diff changeset
222 <param name="compFile" value="SE_comp.g1.vs.g2.txt"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
223 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
224 <!--
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
225 <conditional name="doComp">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
226 <param name="compare_selector" value="1"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
227 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
228 -->
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
229 <param name="output_selector" value="1,2,3,4"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
230 <output name="output1" file="SE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr" ftype="interval" lines_diff="1"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
231 <output name="output2" file="SE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
232 <output_collection name="output_collection_bam" count="4">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
233 <element name="g1_r1.bam" file="SE_g1_r1.bam" compare="sim_size"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
234 <element name="g1_r2.bam" file="SE_g1_r2.bam" compare="sim_size"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
235 <element name="g2_r1.bam" file="SE_g2_r1.bam" compare="sim_size"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
236 <element name="g2_r2.bam" file="SE_g2_r2.bam" compare="sim_size"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
237 </output_collection>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
238 <output_collection name="output_collection_bed" count="2">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
239 <element name="g1.G.bed" file="SE_g1.G.bed" ftype="interval" lines_diff="1"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
240 <element name="g2.G.bed" file="SE_g2.G.bed" ftype="interval" lines_diff="1"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
241 </output_collection>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
242 </test>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
243 <test>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
244 <!-- test paired-end reads -->
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
245 <param name="reference_source_selector" value="history"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
246 <param name="ref_file" ftype="fasta" value="seg.fa"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
247 <repeat name="g1_fastq">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
248 <conditional name="fastq_input">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
249 <param name="fastq_input_selector" value="paired"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
250 <param name="fastq_input1" value="6_all_1.fq.gz"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
251 <param name="fastq_input2" value="6_all_2.fq.gz"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
252 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
253 </repeat>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
254 <repeat name="g2_fastq">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
255 <conditional name="fastq_input">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
256 <param name="fastq_input_selector" value="paired"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
257 <param name="fastq_input1" value="8_all_1.fq.gz"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
258 <param name="fastq_input2" value="8_all_2.fq.gz"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
259 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
260 </repeat>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
261 <conditional name="doComp">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
262 <param name="compare_selector" value="0"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
263 <param name="compFile" value="PE_comp.g1.vs.g2.txt"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
264 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
265 <!--
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
266 <conditional name="doComp">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
267 <param name="compare_selector" value="1"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
268 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
269 -->
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
270 <param name="output_selector" value="1,2"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
271 <output name="output1" file="PE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr" ftype="interval" lines_diff="1"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
272 <output name="output2" file="PE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
273 </test>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
274 <test>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
275 <!-- test paired collection -->
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
276 <param name="reference_source_selector" value="history"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
277 <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
278 <repeat name="g1_fastq">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
279 <conditional name="fastq_input">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
280 <param name="fastq_input_selector" value="paired_collection"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
281 <param name="fastq_input1">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
282 <collection type="paired">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
283 <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
284 <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
285 </collection>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
286 </param>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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287 </conditional>
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288 </repeat>
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289 <repeat name="g2_fastq">
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290 <conditional name="fastq_input">
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291 <param name="fastq_input_selector" value="paired_collection"/>
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292 <param name="fastq_input1">
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293 <collection type="paired">
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294 <element name="forward" value="8_all_1.fq.gz" />
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295 <element name="reverse" value="8_all_2.fq.gz" />
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296 </collection>
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297 </param>
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298 </conditional>
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299 </repeat>
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300 <conditional name="doComp">
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301 <param name="compare_selector" value="0"/>
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302 <param name="compFile" value="PE_comp.g1.vs.g2.txt"/>
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303 </conditional>
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304 <!--
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
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305 <conditional name="doComp">
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306 <param name="compare_selector" value="1"/>
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307 </conditional>
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308 -->
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diff changeset
309 <param name="output_selector" value="1,2"/>
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310 <output name="output1" file="PE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr" ftype="interval" lines_diff="1"/>
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311 <output name="output2" file="PE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/>
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312 </test>
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313 <test>
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parents:
diff changeset
314 <!-- test data table reference -->
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parents:
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315 <param name="reference_source_selector" value="cached"/>
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parents:
diff changeset
316 <param name="ref_file" value="chr11"/>
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parents:
diff changeset
317 <repeat name="g1_fastq">
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parents:
diff changeset
318 <conditional name="fastq_input">
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diff changeset
319 <param name="fastq_input_selector" value="single"/>
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diff changeset
320 <param name="fastq_input1" value="WTPE1.fastq.gz"/>
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parents:
diff changeset
321 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
322 </repeat>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
323 <repeat name="g1_fastq">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
324 <conditional name="fastq_input">
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parents:
diff changeset
325 <param name="fastq_input_selector" value="single"/>
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parents:
diff changeset
326 <param name="fastq_input1" value="WTPE2.fastq.gz"/>
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parents:
diff changeset
327 </conditional>
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parents:
diff changeset
328 </repeat>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
329 <repeat name="g2_fastq">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
330 <conditional name="fastq_input">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
331 <param name="fastq_input_selector" value="single"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
332 <param name="fastq_input1" value="TKO2PE1.fastq.gz"/>
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parents:
diff changeset
333 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
334 </repeat>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
335 <repeat name="g2_fastq">
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
336 <conditional name="fastq_input">
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parents:
diff changeset
337 <param name="fastq_input_selector" value="single"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
338 <param name="fastq_input1" value="TKO2PE2.fastq.gz"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
339 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
340 </repeat>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
341 <conditional name="doComp">
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parents:
diff changeset
342 <param name="compare_selector" value="0"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
343 <param name="compFile" value="SE_comp.g1.vs.g2.txt"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
344 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
345 <!--
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
346 <conditional name="doComp">
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parents:
diff changeset
347 <param name="compare_selector" value="1"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
348 </conditional>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
349 -->
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
350 <param name="output_selector" value="1,2"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
351 <output name="output1" file="SE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr" ftype="interval" lines_diff="1"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
352 <output name="output2" file="SE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
353 </test>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
354 </tests>
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parents:
diff changeset
355 <help>
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iuc
parents:
diff changeset
356 <![CDATA[
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
357 **MOABS: MOdel based Analysis of Bisulfite Sequencing data**
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
358
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
359 MOABS is a comprehensive, accurate and efficient solution for analysis of large
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
360 scale base-resolution DNA methylation data, bisulfite sequencing or single
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
361 molecule direct sequencing.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
362
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
363 MOABS seamlessly integrates alignment, methylation calling, identification of
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
364 hypomethylation for one sample and differential methylation for multiple
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
365 samples, and other downstream analysis.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
366
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
367 For more information, check https://github.com/sunnyisgalaxy/moabs.
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parents:
diff changeset
368
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
369 -----
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
370
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
371 **Input files**
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
372
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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parents:
diff changeset
373 MOABS needs to input Bisulfite sequencing reads in two groups of interest, e.g.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
374 KO vs WT. Each group of reads may have combined sequencing library, i.e.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
375 single-end reads and/or paired-end reads. Multiple replicates can be specified in each group.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
376
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
377 **Outputs**
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parents:
diff changeset
378
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
379 Four output files can be selected to report, namely
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
380
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
381 1. **DMR region file** - the major result file
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
382 2. **Comparison file between two groups** - the intermediate comparion result
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
383 3. **BAM files** - intermediate BAM files
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
384 4. **Methylation BED files** - intermediate methylation BED files
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
385
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
diff changeset
386 -----
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
iuc
parents:
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387
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388 MOABS will detect differential methylated regions (DMRs) using the input BS-Seq
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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389 reads. The output file is a tab-delimited text file (not strictly a BED
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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390 format), representing DMRs. It has 8 columns as below.
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391
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392 chrom<TAB>start<TAB>end<TAB>methylation_state<TAB>CpGsites<TAB>DMCcount<TAB>nonDMCcount<TAB>hidden_state
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393
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394 1. **chrom** - The chromosome of the region.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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395 2. **start** - The start genomic locus of the region.
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396 3. **end** - The end genomic locus of the region.
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397 4. **methylation_state** - The methylation state of the region, "+"/"-" representing hyper- or hypo-methylation regions.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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398 5. **CpGsites** - Total number of CpG sites in the region.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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399 6. **DMCcount** - The number of differential methylated CpG sites (DMCs) in the region.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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400 7. **nonDMCcount** - The number of non-DMCs in the region.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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401 8. **hidden_state** - The hidden state prediced by Hidden Markov Model (HMM), "1"/"-1" representing hyper- or hypo-methylation states.
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402
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403 For example, six DMRs are identified in the following format.
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404
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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405 @DMRExample@
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406
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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407 -----
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408
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409 The intermediate comparison file summarizes methylation ratio comparison
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410 results on CpG sites. It has 19 columns as below.
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411
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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412 1. **chrom** - The chromosome of the GpG site.
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413 2. **start** - The start position of the site.
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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414 3. **end** - The end position of the site.
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415 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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416 5. **totalC_0** - Total number of Cs in the first group.
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417 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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418 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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419 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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420 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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421 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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422 11. **ratioCI_1** - The confidence interval of the methylation ratio in the second group.
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423 12. **pair** - The next three columns are attributes for pairs of groups.
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424 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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425 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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426 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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427 16. **p_sim** - The next column is the simulation p-value.
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428 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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429 18. **p_fet** - The next column is the FET p-value.
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430 19. **p_fet_1_v_0** - FET p-value between group 1 and group 0.
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431
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432 The comparison result file can be reused for DMR calling.
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433
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434 -----
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435
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436 BAM files are intermediate mapping results of input reads to the referene
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437 genome. These BAM files can be reused in downstream methylation analysis.
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438
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439 -----
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440
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441 Methylation calling BED files are intermediate methylation calling results of
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442 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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443 reused in downstream DMR calling and visualization. The BED file has 15 columns
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444 as below.
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445
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446 1. **chrom** - The chromosome of the site.
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447 2. **start** - The start position of the site.
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448 3. **end** - The end position of the site.
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449 4. **ratio** - Methylation ratio in the site
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450 5. **totalC** - Total number of reads in current Cs.
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451 6. **methC** - Methylated Cs.
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452 7. **strand** - The strand information for prevous three columns.
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453 8. **next** - The next base.
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454 9. **Plus** - Next two columns are for forward strand.
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455 10. **totalC** - Total number of Cs.
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456 11. **methC** - Methylated Cs.
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457 12. **Minus** - Next two columns are for reverse strand.
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458 13. **totalC** - Total number of Cs.
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459 14. **methC** - Methylated Cs.
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460 15. **localSeq** - Local sequences.
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461
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462 ]]>
26d7ec4af119 "planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845"
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463 </help>
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464 <expand macro="citations"/>
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465 </tool>