Mercurial > repos > davidvanzessen > sff_extract_demultiplex
view demultiplex.xml @ 0:cb08a27e5fc2 draft
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author | davidvanzessen |
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date | Mon, 29 Aug 2016 05:44:57 -0400 |
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children | cbce7f35f8b0 |
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<tool id="demultiplex" name="Demultiplex" version="1.0"> <description> </description> <requirements> <requirement type="package" version="0.0.13">fastx_toolkit</requirement> </requirements> <command interpreter="bash"> wrapper.sh "$input" "$out_file" "$out_file.files_path" "$where" "$mismatches" "$partial" "$input.name" #for $i, $b in enumerate($barcodes) "$b.id" "$b.mid" "$b.trim_start" "$b.trim_end" #end for </command> <inputs> <param name="input" type="data" label="File to split" /> <repeat name="barcodes" title="Barcodes" min="1" default="1"> <param name="id" type="text" size="50" label="ID" /> <param name="mid" type="select" label="Mid"> <option value="ACGAGTGCGT">MID-1</option> <option value="ACGCACTCGT">MID-1 reverse complement</option> <option value="ACGCTCGACA">MID-2</option> <option value="TGTCGAGCGT">MID-2 reverse complement</option> <option value="AGACGCACTC">MID-3</option> <option value="GAGTGCGTCT">MID-3 reverse complement</option> <option value="AGCACTGTAG">MID-4</option> <option value="CTACAGTGCT">MID-4 reverse complement</option> <option value="ATCAGACACG">MID-5</option> <option value="CGTGTCTGAT">MID-5 reverse complement</option> <option value="ATATCGCGAG">MID-6</option> <option value="CTCGCGATAT">MID-6 reverse complement</option> <option value="CGTGTCTCTA">MID-7</option> <option value="TAGAGACACG">MID-7 reverse complement</option> <option value="CTCGCGTGTC">MID-8</option> <option value="GACACGCGAG">MID-8 reverse complement</option> <option value="TCTCTATGCG">MID-10</option> <option value="CGCATAGAGA">MID-10 reverse complement</option> <option value="TGATACGTCT">MID-11</option> <option value="AGACGTATCA">MID-11 reverse complement</option> <option value="CATAGTAGTG">MID-13</option> <option value="CACTACTATG">MID-13 reverse complement</option> <option value="CGAGAGATAC">MID-14</option> <option value="GTATCTCTCG">MID-14 reverse complement</option> <option value="ATACGACGTA">MID-15</option> <option value="TACGTCGTAT">MID-15 reverse complement</option> <option value="TCACGTACTA">MID-16</option> <option value="TAGTACGTGA">MID-16 reverse complement</option> <option value="CGTCTAGTAC">MID-17</option> <option value="GTACTAGACG">MID-17 reverse complement</option> <option value="TCTACGTAGC">MID-18</option> <option value="GCTACGTAGA">MID-18 reverse complement</option> <option value="TGTACTACTC">MID-19</option> <option value="GAGTAGTACA">MID-19 reverse complement</option> <option value="ACGACTACAG">MID-20</option> <option value="CTGTAGTCGT">MID-20 reverse complement</option> <option value="CGTAGACTAG">MID-21</option> <option value="CTAGTCTACG">MID-21 reverse complement</option> <option value="TACGAGTATG">MID-22</option> <option value="CATACTCGTA">MID-22 reverse complement</option> <option value="TACTCTCGTG">MID-23</option> <option value="CACGAGAGTA">MID-23 reverse complement</option> <option value="TAGAGACGAG">MID-24</option> <option value="CTCGTCTCTA">MID-24 reverse complement</option> <option value="TCGTCGCTCG">MID-25</option> <option value="CGAGCGACGA">MID-25 reverse complement</option> <option value="ACATACGCGT">MID-26</option> <option value="ACGCGTATGT">MID-26 reverse complement</option> <option value="ACGCGAGTAT">MID-27</option> <option value="ATACTCGCGT">MID-27 reverse complement</option> <option value="ACTACTATGT">MID-28</option> <option value="ACATAGTAGT">MID-28 reverse complement</option> <option value="ACTGTACAGT">MID-29</option> <option value="ACTGTACAGT">MID-29 reverse complement</option> <option value="AGACTATACT">MID-30</option> <option value="AGTATAGTCT">MID-30 reverse complement</option> <option value="AGCGTCGTCT">MID-31</option> <option value="AGACGACGCT">MID-31 reverse complement</option> <option value="AGTACGCTAT">MID-32</option> <option value="ATAGCGTACT">MID-32 reverse complement</option> <option value="ATAGAGTACT">MID-33</option> <option value="AGTACTCTAT">MID-33 reverse complement</option> <option value="CACGCTACGT">MID-34</option> <option value="ACGTAGCGTG">MID-34 reverse complement</option> <option value="CAGTAGACGT">MID-35</option> <option value="ACGTCTACTG">MID-35 reverse complement</option> <option value="CGACGTGACT">MID-36</option> <option value="AGTCACGTCG">MID-36 reverse complement</option> <option value="TACACACACT">MID-37</option> <option value="AGTGTGTGTA">MID-37 reverse complement</option> <option value="TACACGTGAT">MID-38</option> <option value="ATCACGTGTA">MID-38 reverse complement</option> <option value="TACAGATCGT">MID-39</option> <option value="ACGATCTGTA">MID-39 reverse complement</option> <option value="TACGCTGTCT">MID-40</option> <option value="AGACAGCGTA">MID-40 reverse complement</option> <option value="TAGTGTAGAT">MID-41</option> <option value="ATCTACACTA">MID-41 reverse complement</option> <option value="TCGATCACGT">MID-42</option> <option value="ACGTGATCGA">MID-42 reverse complement</option> <option value="TCGCACTAGT">MID-43</option> <option value="ACTAGTGCGA">MID-43 reverse complement</option> <option value="TCTAGCGACT">MID-44</option> <option value="AGTCGCTAGA">MID-44 reverse complement</option> <option value="TCTATACTAT">MID-45</option> <option value="ATAGTATAGA">MID-45 reverse complement</option> <option value="TGACGTATGT">MID-46</option> <option value="ACATACGTCA">MID-46 reverse complement</option> <option value="TGTGAGTAGT">MID-47</option> <option value="ACTACTCACA">MID-47 reverse complement</option> <option value="ACAGTATATA">MID-48</option> <option value="TATATACTGT">MID-48 reverse complement</option> <option value="ACGCGATCGA">MID-49</option> <option value="TCGATCGCGT">MID-49 reverse complement</option> <option value="ACTAGCAGTA">MID-50</option> <option value="TACTGCTAGT">MID-50 reverse complement</option> <option value="AGCTCACGTA">MID-51</option> <option value="TACGTGAGCT">MID-51 reverse complement</option> <option value="AGTATACATA">MID-52</option> <option value="TATGTATACT">MID-52 reverse complement</option> <option value="AGTCGAGAGA">MID-53</option> <option value="TCTCTCGACT">MID-53 reverse complement</option> <option value="AGTGCTACGA">MID-54</option> <option value="TCGTAGCACT">MID-54 reverse complement</option> <option value="CGATCGTATA">MID-55</option> <option value="TATACGATCG">MID-55 reverse complement</option> <option value="CGCAGTACGA">MID-56</option> <option value="TCGTACTGCG">MID-56 reverse complement</option> <option value="CGCGTATACA">MID-57</option> <option value="TGTATACGCG">MID-57 reverse complement</option> <option value="CGTACAGTCA">MID-58</option> <option value="TGACTGTACG">MID-58 reverse complement</option> <option value="CGTACTCAGA">MID-59</option> <option value="TCTGAGTACG">MID-59 reverse complement</option> <option value="CTACGCTCTA">MID-60</option> <option value="TAGAGCGTAG">MID-60 reverse complement</option> <option value="CTATAGCGTA">MID-61</option> <option value="TACGCTATAG">MID-61 reverse complement</option> <option value="TACGTCATCA">MID-62</option> <option value="TGATGACGTA">MID-62 reverse complement</option> <option value="TAGTCGCATA">MID-63</option> <option value="TATGCGACTA">MID-63 reverse complement</option> <option value="TATATATACA">MID-64</option> <option value="TGTATATATA">MID-64 reverse complement</option> <option value="TATGCTAGTA">MID-65</option> <option value="TACTAGCATA">MID-65 reverse complement</option> <option value="TCACGCGAGA">MID-66</option> <option value="TCTCGCGTGA">MID-66 reverse complement</option> <option value="TCGATAGTGA">MID-67</option> <option value="TCACTATCGA">MID-67 reverse complement</option> <option value="TCGCTGCGTA">MID-68</option> <option value="TACGCAGCGA">MID-68 reverse complement</option> <option value="TCTGACGTCA">MID-69</option> <option value="TGACGTCAGA">MID-69 reverse complement</option> <option value="TGAGTCAGTA">MID-70</option> <option value="TACTGACTCA">MID-70 reverse complement</option> <option value="TGTAGTGTGA">MID-71</option> <option value="TCACACTACA">MID-71 reverse complement</option> <option value="TGTCACACGA">MID-72</option> <option value="TCGTGTGACA">MID-72 reverse complement</option> <option value="TGTCGTCGCA">MID-73</option> <option value="TGCGACGACA">MID-73 reverse complement</option> <option value="ACACATACGC">MID-74</option> <option value="GCGTATGTGT">MID-74 reverse complement</option> <option value="ACAGTCGTGC">MID-75</option> <option value="GCACGACTGT">MID-75 reverse complement</option> <option value="ACATGACGAC">MID-76</option> <option value="GTCGTCATGT">MID-76 reverse complement</option> <option value="ACGACAGCTC">MID-77</option> <option value="GAGCTGTCGT">MID-77 reverse complement</option> <option value="ACGTCTCATC">MID-78</option> <option value="GATGAGACGT">MID-78 reverse complement</option> <option value="ACTCATCTAC">MID-79</option> <option value="GTAGATGAGT">MID-79 reverse complement</option> <option value="ACTCGCGCAC">MID-80</option> <option value="GTGCGCGAGT">MID-80 reverse complement</option> <option value="AGAGCGTCAC">MID-81</option> <option value="GTGACGCTCT">MID-81 reverse complement</option> <option value="AGCGACTAGC">MID-82</option> <option value="GCTAGTCGCT">MID-82 reverse complement</option> <option value="AGTAGTGATC">MID-83</option> <option value="GATCACTACT">MID-83 reverse complement</option> <option value="AGTGACACAC">MID-84</option> <option value="GTGTGTCACT">MID-84 reverse complement</option> <option value="AGTGTATGTC">MID-85</option> <option value="GACATACACT">MID-85 reverse complement</option> <option value="ATAGATAGAC">MID-86</option> <option value="GTCTATCTAT">MID-86 reverse complement</option> <option value="ATATAGTCGC">MID-87</option> <option value="GCGACTATAT">MID-87 reverse complement</option> <option value="ATCTACTGAC">MID-88</option> <option value="GTCAGTAGAT">MID-88 reverse complement</option> <option value="CACGTAGATC">MID-89</option> <option value="GATCTACGTG">MID-89 reverse complement</option> <option value="CACGTGTCGC">MID-90</option> <option value="GCGACACGTG">MID-90 reverse complement</option> <option value="CATACTCTAC">MID-91</option> <option value="GTAGAGTATG">MID-91 reverse complement</option> <option value="CGACACTATC">MID-92</option> <option value="GATAGTGTCG">MID-92 reverse complement</option> <option value="CGAGACGCGC">MID-93</option> <option value="GCGCGTCTCG">MID-93 reverse complement</option> <option value="CGTATGCGAC">MID-94</option> <option value="GTCGCATACG">MID-94 reverse complement</option> <option value="CGTCGATCTC">MID-95</option> <option value="GAGATCGACG">MID-95 reverse complement</option> <option value="CTACGACTGC">MID-96</option> <option value="GCAGTCGTAG">MID-96 reverse complement</option> <option value="CTAGTCACTC">MID-97</option> <option value="GAGTGACTAG">MID-97 reverse complement</option> <option value="CTCTACGCTC">MID-98</option> <option value="GAGCGTAGAG">MID-98 reverse complement</option> <option value="CTGTACATAC">MID-99</option> <option value="GTATGTACAG">MID-99 reverse complement</option> <option value="TAGACTGCAC">MID-100</option> <option value="GTGCAGTCTA">MID-100 reverse complement</option> <option value="TAGCGCGCGC">MID-101</option> <option value="GCGCGCGCTA">MID-101 reverse complement</option> <option value="TAGCTCTATC">MID-102</option> <option value="GATAGAGCTA">MID-102 reverse complement</option> <option value="TATAGACATC">MID-103</option> <option value="GATGTCTATA">MID-103 reverse complement</option> <option value="TATGATACGC">MID-104</option> <option value="GCGTATCATA">MID-104 reverse complement</option> <option value="TCACTCATAC">MID-105</option> <option value="GTATGAGTGA">MID-105 reverse complement</option> <option value="TCATCGAGTC">MID-106</option> <option value="GACTCGATGA">MID-106 reverse complement</option> <option value="TCGAGCTCTC">MID-107</option> <option value="GAGAGCTCGA">MID-107 reverse complement</option> <option value="TCGCAGACAC">MID-108</option> <option value="GTGTCTGCGA">MID-108 reverse complement</option> <option value="TCTGTCTCGC">MID-109</option> <option value="GCGAGACAGA">MID-109 reverse complement</option> <option value="TGAGTGACGC">MID-110</option> <option value="GCGTCACTCA">MID-110 reverse complement</option> <option value="TGATGTGTAC">MID-111</option> <option value="GTACACATCA">MID-111 reverse complement</option> <option value="TGCTATAGAC">MID-112</option> <option value="GTCTATAGCA">MID-112 reverse complement</option> <option value="TGCTCGCTAC">MID-113</option> <option value="GTAGCGAGCA">MID-113 reverse complement</option> <option value="ACGTGCAGCG">MID-114</option> <option value="CGCTGCACGT">MID-114 reverse complement</option> <option value="ACTCACAGAG">MID-115</option> <option value="CTCTGTGAGT">MID-115 reverse complement</option> <option value="AGACTCAGCG">MID-116</option> <option value="CGCTGAGTCT">MID-116 reverse complement</option> <option value="AGAGAGTGTG">MID-117</option> <option value="CACACTCTCT">MID-117 reverse complement</option> <option value="AGCTATCGCG">MID-118</option> <option value="CGCGATAGCT">MID-118 reverse complement</option> <option value="AGTCTGACTG">MID-119</option> <option value="CAGTCAGACT">MID-119 reverse complement</option> <option value="AGTGAGCTCG">MID-120</option> <option value="CGAGCTCACT">MID-120 reverse complement</option> <option value="ATAGCTCTCG">MID-121</option> <option value="CGAGAGCTAT">MID-121 reverse complement</option> <option value="ATCACGTGCG">MID-122</option> <option value="CGCACGTGAT">MID-122 reverse complement</option> <option value="ATCGTAGCAG">MID-123</option> <option value="CTGCTACGAT">MID-123 reverse complement</option> <option value="ATCGTCTGTG">MID-124</option> <option value="CACAGACGAT">MID-124 reverse complement</option> <option value="ATGTACGATG">MID-125</option> <option value="CATCGTACAT">MID-125 reverse complement</option> <option value="ATGTGTCTAG">MID-126</option> <option value="CTAGACACAT">MID-126 reverse complement</option> <option value="CACACGATAG">MID-127</option> <option value="CTATCGTGTG">MID-127 reverse complement</option> <option value="CACTCGCACG">MID-128</option> <option value="CGTGCGAGTG">MID-128 reverse complement</option> <option value="CAGACGTCTG">MID-129</option> <option value="CAGACGTCTG">MID-129 reverse complement</option> <option value="CAGTACTGCG">MID-130</option> <option value="CGCAGTACTG">MID-130 reverse complement</option> <option value="CGACAGCGAG">MID-131</option> <option value="CTCGCTGTCG">MID-131 reverse complement</option> <option value="CGATCTGTCG">MID-132</option> <option value="CGACAGATCG">MID-132 reverse complement</option> <option value="CGCGTGCTAG">MID-133</option> <option value="CTAGCACGCG">MID-133 reverse complement</option> <option value="CGCTCGAGTG">MID-134</option> <option value="CACTCGAGCG">MID-134 reverse complement</option> <option value="CGTGATGACG">MID-135</option> <option value="CGTCATCACG">MID-135 reverse complement</option> <option value="CTATGTACAG">MID-136</option> <option value="CTGTACATAG">MID-136 reverse complement</option> <option value="CTCGATATAG">MID-137</option> <option value="CTATATCGAG">MID-137 reverse complement</option> <option value="CTCGCACGCG">MID-138</option> <option value="CGCGTGCGAG">MID-138 reverse complement</option> <option value="CTGCGTCACG">MID-139</option> <option value="CGTGACGCAG">MID-139 reverse complement</option> <option value="CTGTGCGTCG">MID-140</option> <option value="CGACGCACAG">MID-140 reverse complement</option> <option value="TAGCATACTG">MID-141</option> <option value="CAGTATGCTA">MID-141 reverse complement</option> <option value="TATACATGTG">MID-142</option> <option value="CACATGTATA">MID-142 reverse complement</option> <option value="TATCACTCAG">MID-143</option> <option value="CTGAGTGATA">MID-143 reverse complement</option> <option value="TATCTGATAG">MID-144</option> <option value="CTATCAGATA">MID-144 reverse complement</option> <option value="TCGTGACATG">MID-145</option> <option value="CATGTCACGA">MID-145 reverse complement</option> <option value="TCTGATCGAG">MID-146</option> <option value="CTCGATCAGA">MID-146 reverse complement</option> <option value="TGACATCTCG">MID-147</option> <option value="CGAGATGTCA">MID-147 reverse complement</option> <option value="TGAGCTAGAG">MID-148</option> <option value="CTCTAGCTCA">MID-148 reverse complement</option> <option value="TGATAGAGCG">MID-149</option> <option value="CGCTCTATCA">MID-149 reverse complement</option> <option value="TGCGTGTGCG">MID-150</option> <option value="CGCACACGCA">MID-150 reverse complement</option> <option value="TGCTAGTCAG">MID-151</option> <option value="CTGACTAGCA">MID-151 reverse complement</option> <option value="TGTATCACAG">MID-152</option> <option value="CTGTGATACA">MID-152 reverse complement</option> <option value="TGTGCGCGTG">MID-153</option> <option value="CACGCGCACA">MID-153 reverse complement</option> </param> <param name="trim_start" type="integer" size="3" value="0" label="How many nucleotides to trim from the start" /> <param name="trim_end" type="integer" size="3" value="0" label="How many nucleotides to trim from the end" /> </repeat> <param name="where" type="select" label="Barcodes found at"> <option value="bol">Start: 5' end</option> <option value="eol">End: 3' end</option> </param> <param name="mismatches" type="integer" size="3" value="2" label="Max. number of mismatches allowed." /> <param name="partial" type="integer" size="3" value="0" label="Allow partial overlap of barcodes." /> </inputs> <outputs> <data format="html" name="out_file" /> </outputs> <help> - Splitting sff or fastq files into FASTQ, FASTA and (optional) trimmed FASTA files with a FASTQC report on the FASTQ file, this tool uses: - sff2fastq (https://github.com/indraniel/sff2fastq) to extract a fastq file. - fastx_barcode_splitter.pl (http://hannonlab.cshl.edu/fastx_toolkit/commandline.html) to demultiplex. - fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to provide analysis of the fastq files. </help> </tool>