Mercurial > repos > iuc > qiime_filter_fasta
annotate filter_fasta.xml @ 1:615e7553998c 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 03:51:22 -0400 |
parents | 794553858db3 |
children | 82ab467a74fc |
rev | line source |
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0
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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1 <tool id="qiime_filter_fasta" name="Filter fasta" version="@WRAPPER_VERSION@.0"> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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2 <description>to remove sequences based on input criteria</description> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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3 <macros> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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5 </macros> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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6 <expand macro="requirements"/> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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7 <command detect_errors="aggressive"><![CDATA[ |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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8 filter_fasta.py |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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9 --input_fasta_fp '$input_fasta_fp' |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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10 --output_fasta_fp '$fitered_fasta' |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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11 #if $selection.type == "otu_map" |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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12 --otu_map '$selection.otu_map' |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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13 #else if $selection.type == "seq_list" |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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14 --seq_id_fp '$selection.seq_id_fp' |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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15 #else if $selection.type == "biom" |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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16 --biom_fp '$selection.biom_fp' |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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17 #else if $selection.type == "fasta" |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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18 --subject_fasta_fp '$selection.subject_fasta_fp' |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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19 #else if $selection.type == "prefix" |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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20 --seq_id_prefix '$selection.seq_id_prefix' |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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21 #else if $selection.type == "prefix_list" |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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22 --sample_id_fp '$selection.sample_id_fp' |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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23 #else if $selection.type == "valid_states" |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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24 --mapping_fp '$selection.mapping_fp' |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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25 --valid_states '$selection.valid_states' |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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26 #end if |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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27 $negate |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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28 ]]></command> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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29 <inputs> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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30 <param name="input_fasta_fp" argument="--input_fasta_fp" type="data" format="fasta" label="Input fasta file"/> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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31 <conditional name="selection"> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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32 <param name="type" label="Type of criteria for filtering" type="select"> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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33 <option value="otu_map">OTU map-based filtering</option> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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34 <option value="seq_list">Filtering using a list of sequence identifiers</option> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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35 <option value="biom">Filtering based on OTU identifiers in a BIOM file</option> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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36 <option value="fasta">Filtering based on sequence identifiers in a Fasta file</option> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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37 <option value="prefix">Filtering based on a sequence id prefix</option> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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38 <option value="prefix_list">Filtering based on a list of sequence id prefix</option> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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39 <option value="valid_states">Filtering based on a sample id description</option> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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40 </param> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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41 <when value="otu_map"> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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42 <param argument="--otu_map" type="data" format="txt" label="OTU map where sequences ids are those which should be retained"/> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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43 </when> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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44 <when value="seq_list"> |
794553858db3
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="--seq_id_fp" type="data" format="tabular,tsv,csv,txt" label="List of sequence identifiers (or tab-delimited lines with a seq identifier in the first field) which should be retained"/> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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46 </when> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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47 <when value="biom"> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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48 <param argument="--biom_fp" type="data" format="biom1" label="Biom file with OTU identifiers that should be retained"/> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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49 </when> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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50 <when value="fasta"> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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51 <param argument="--subject_fasta_fp" type="data" format="fasta" label="Fasta file where the seq ids should be retained"/> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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52 </when> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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53 <when value="prefix"> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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54 <param argument="--seq_id_prefix" type="text" label="Prefix to keep seqs where seq_id starts with this prefix"/> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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55 </when> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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56 <when value="prefix_list"> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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57 <param argument="--sample_id_fp" type="data" format="txt" label="List of prefix to keep seqs where seq_id starts with a sample id listed in this file"/> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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58 </when> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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59 <when value="valid_states"> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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60 <param argument="--mapping_fp" type="data" format="txt" label="Mapping file"/> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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61 <param argument="--valid_states" type="text" label="Description of the sample ids to retain"/> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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62 </when> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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63 </conditional> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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64 <param argument="--negate" type="boolean" truevalue="--negate" falsevalue="" checked="False" label="Discard passed seq ids rather than keep passed seq ids?"/> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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65 </inputs> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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66 <outputs> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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67 <data name="fitered_fasta" format="fasta" label="${tool.name} on ${on_string}: Filtered sequences"/> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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68 </outputs> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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69 <tests> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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70 <test> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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71 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> |
794553858db3
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="type" value="otu_map"/> |
794553858db3
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="otu_map" value="filter_fasta/otu_map.txt"/> |
794553858db3
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="negate" value=""/> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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75 <output name="fitered_fasta" md5="9185f3cdcba8bcaf159cc3f1fdbb5ebb"/> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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76 </test> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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77 <test> |
794553858db3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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78 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> |
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79 <param name="type" value="otu_map"/> |
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80 <param name="otu_map" value="filter_fasta/otu_map.txt"/> |
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81 <param name="negate" value="--negate"/> |
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82 <output name="fitered_fasta" md5="206a5c83e5abbd674f632da73ec518a2"/> |
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83 </test> |
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84 <test> |
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85 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> |
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86 <param name="type" value="seq_list"/> |
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87 <param name="seq_id_fp" value="filter_fasta/seqs_to_keep.txt"/> |
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88 <param name="negate" value=""/> |
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89 <output name="fitered_fasta" md5="19ba95928ca9419f671810240120c8cd"/> |
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90 </test> |
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91 <test> |
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92 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> |
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93 <param name="type" value="biom"/> |
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94 <param name="biom_fp" value="filter_fasta/otu_table.biom"/> |
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95 <param name="negate" value=""/> |
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96 <output name="fitered_fasta" md5="d41d8cd98f00b204e9800998ecf8427e"/> |
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97 </test> |
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98 <test> |
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99 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> |
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100 <param name="type" value="fasta"/> |
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101 <param name="subject_fasta_fp" value="filter_fasta/sl_inseqs.fasta"/> |
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102 <param name="negate" value=""/> |
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103 <output name="fitered_fasta" md5="9c5f416e94bcfb2d4003ea002cbaf617"/> |
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104 </test> |
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105 <test> |
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106 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> |
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107 <param name="type" value="prefix"/> |
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108 <param name="seq_id_prefix" value="S5"/> |
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109 <param name="negate" value=""/> |
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110 <output name="fitered_fasta" md5="c1f2d8c5844733f30ca07547846c4d36"/> |
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111 </test> |
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112 <test> |
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113 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> |
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114 <param name="type" value="prefix_list"/> |
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115 <param name="sample_id_fp" value="filter_fasta/map.txt"/> |
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116 <param name="negate" value=""/> |
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117 <output name="fitered_fasta" md5="8f0025b067d22ed708ee55de10016785"/> |
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118 </test> |
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119 </tests> |
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120 <help><![CDATA[ |
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121 **What it does** |
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122 |
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123 Filter fasta or fastq file to remove sequences based on input criteria |
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124 ]]></help> |
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125 <citations> |
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126 <expand macro="citations"/> |
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127 </citations> |
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128 </tool> |