Mercurial > repos > iuc > qiime_multiple_split_libraries_fastq
annotate multiple_split_libraries_fastq.xml @ 1:33a751525a8f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 03:53:11 -0400 |
parents | 0a7b6f4036dd |
children | a8bff14347ec |
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0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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1 <tool id="qiime_multiple_split_libraries_fastq" name="Split multiple FastQ librairies" version="@WRAPPER_VERSION@.0"> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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2 <description>to performs demultiplexing</description> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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3 <macros> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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4 <import>macros.xml</import> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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5 </macros> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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6 <expand macro="requirements"/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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7 <version_command>multiple_split_libraries_fastq.py -v</version_command> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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8 <command detect_errors="aggressive"><![CDATA[ |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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9 mkdir input |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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10 && |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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11 #for $i, $s in enumerate( $input_files ) |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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12 ln -s '$s.reads' input/reads_${i}.fastq |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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13 && |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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14 ln -s '$s.barcodes' input/barcodes_${i}.fastq |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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15 && |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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16 ln -s '$s.mapping' input/mapping_${i}.txt |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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17 && |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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18 #end for |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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19 multiple_split_libraries_fastq.py |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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20 --input_dir 'input' |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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21 --output_dir 'output' |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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22 --demultiplexing_method 'mapping_barcode_files' |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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23 #if $parameter_fp |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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24 --parameter_fp '$parameter_fp' |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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25 #end if |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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26 --read_indicator 'reads_' |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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27 --barcode_indicator 'barcodes_' |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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28 --mapping_indicator 'mapping_' |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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29 --mapping_extensions 'txt' |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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30 --leading_text '$leading_text' |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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31 --trailing_text '$trailing_text' |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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32 --sampleid_indicator '.' |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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33 ]]></command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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34 <inputs> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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35 <repeat name="input_files" title="Input files"> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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36 <param name="reads" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Read file"/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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37 <param name="barcodes" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Barcode file"/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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38 <param name="mapping" type="data" format="txt,tsv,tabular" label="Mapping file"/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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39 </repeat> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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40 <param argument="--demultiplexing_method" type="select" label="Method for demultiplexing"> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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41 <!--<option value="sampleid_by_file" selected="true">Each read file will be used to generate the –sample_ids value passed to split_libraries_fastq.py</option>--> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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42 <option value="mapping_barcode_file">Search for barcodes and mapping files that match the input read files</option> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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43 </param> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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44 <param argument="--parameter_fp" type="data" format="txt" label="Parameter file" help="It specifies changes to the default behavior of join_paired_ends.py" optional="true"/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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45 <param argument="--leading_text" type="text" value="" label="Leading text to add to each join_paired_ends.py command"/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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46 <param argument="--trailing_text" type="text" value="" label="Trailing text to add to each join_paired_ends.py command"/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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47 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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48 <outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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49 <data name="seq" format="fastq" label="${tool.name} on ${on_string}: Sequences" from_work_dir="output/seqs.fna" /> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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50 <data name="histogram" format="txt" from_work_dir="output/histograms.txt" label="${tool.name} on ${on_string}: Histograms"/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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51 <data name="log" format="txt" from_work_dir="output/log_*" label="${tool.name} on ${on_string}: Log"/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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52 </outputs> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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53 <tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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54 <test> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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55 <repeat name="input_files"> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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56 <param name="reads" value="multiple_split_libraries_fastq/input/reads_1.fastq"/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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57 <param name="barcodes" value="multiple_split_libraries_fastq/input/barcodes_1.fastq"/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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58 <param name="mapping" value="multiple_split_libraries_fastq/input/mapping_1.txt"/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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59 </repeat> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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60 <repeat name="input_files"> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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61 <param name="reads" value="multiple_split_libraries_fastq/input/reads_2.fastq"/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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62 <param name="barcodes" value="multiple_split_libraries_fastq/input/barcodes_2.fastq"/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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63 <param name="mapping" value="multiple_split_libraries_fastq/input/mapping_2.txt"/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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64 </repeat> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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65 <param name="leading_text" value=""/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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66 <param name="trailing_text" value=""/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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67 <output name="seq" md5="c146828efa459ec7227fcbcd6e5d4cdc"/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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68 <output name="histogram" md5="5f1f73dded81cbed9f1892aabdc2cbb3"/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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69 </test> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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70 <test> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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71 <repeat name="input_files"> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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72 <param name="reads" value="multiple_split_libraries_fastq/input/reads_1.fastq"/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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73 <param name="barcodes" value="multiple_split_libraries_fastq/input/barcodes_1.fastq"/> |
0a7b6f4036dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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74 <param name="mapping" value="multiple_split_libraries_fastq/input/mapping_1.txt"/> |
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75 </repeat> |
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76 <repeat name="input_files"> |
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77 <param name="reads" value="multiple_split_libraries_fastq/input/reads_2.fastq"/> |
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78 <param name="barcodes" value="multiple_split_libraries_fastq/input/barcodes_2.fastq"/> |
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79 <param name="mapping" value="multiple_split_libraries_fastq/input/mapping_2.txt"/> |
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80 </repeat> |
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81 <param name="parameter_fp" value="multiple_split_libraries_fastq/qiime_parameters.txt" /> |
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82 <param name="leading_text" value=""/> |
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83 <param name="trailing_text" value=""/> |
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84 <output name="seq" md5="c146828efa459ec7227fcbcd6e5d4cdc"/> |
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85 <output name="histogram" md5="5f1f73dded81cbed9f1892aabdc2cbb3"/> |
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86 </test> |
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87 </tests> |
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88 <help><![CDATA[ |
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89 **What it does** |
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90 |
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91 In addition to using PCoA, it can be useful to cluster samples using UPGMA (Unweighted Pair Group Method with Arithmetic mean, also known as average linkage). As with PCoA, the input to this step is a distance matrix (i.e. resulting file from beta_diversity.py). |
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92 The output is a newick formatted tree compatible with most standard tree viewing programs. Batch processing is also available, allowing the analysis of an entire directory of distance matrices. |
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93 ]]></help> |
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94 <citations> |
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95 <expand macro="citations"/> |
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96 </citations> |
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97 </tool> |