Mercurial > repos > devteam > fasta_compute_length

annotate fasta_compute_length.xml @ 3:19caae8fd9d4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
author devteam
date Wed, 11 Sep 2019 09:41:36 -0400
parents d75972d4bd2a
children 79cd53e23207
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rev   line source
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19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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1 <?xml version="1.0"?>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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2 <tool id="fasta_compute_length" name="Compute sequence length" version="1.0.2">
2
d75972d4bd2a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6e148b31fed1b322ce720804d8525088ec6d43f9
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3 <description></description>
3
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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4 <command>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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5 #if $ref.ref_source == 'dbkey':
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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6 cp '${ref.index.fields.len_path}' '$output'
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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7 #else:
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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8 python $__tool_directory__/fasta_compute_length.py
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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9 #if $ref.ref_source == 'history':
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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10 '$input'
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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11 #else:
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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12 '${ref.index.fields.path}'
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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13 #end if
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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14 '$output'
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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15 $ref.keep_first
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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16 $ref.keep_first_word
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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17 #end if
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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18 </command>
2
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19 <inputs>
3
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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20 <conditional name="ref">
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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21 <param name="ref_source" type="select" label="Sequences">
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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22 <option value="history" selected="True">From History</option>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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23 <option value="dbkey">Locally Cached (pre-built length files)</option>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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24 <option value="fasta">Locally Cached (full genomes)</option>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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25 </param>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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26 <when value="history">
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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27 <param name="input" type="data" format="fasta" label="Compute length for these sequences"/>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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28 <param name="keep_first" type="integer" value="0" label="How many title characters to keep?" help="'0' = keep the whole thing"/>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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29 <param name="keep_first_word" type="boolean" truevalue="id_only" falsevalue="id_and_desc"
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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30 label="Strip fasta description from header?"
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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31 help="Stripping the description will truncate the fasta header to just the sequence ID. Otherwise the header description will be kept. This step is done before the 'How many characters to keep' option."/>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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32 </when>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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33 <when value="dbkey">
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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34 <param name="index" type="select" label="Source Genome Build">
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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35 <options from_data_table="__dbkeys__"/>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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36 </param>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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37 </when>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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38 <when value="fasta">
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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39 <param name="index" type="select" label="Source Genome Build">
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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40 <options from_data_table="all_fasta"/>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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41 </param>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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42 <param name="keep_first" type="integer" value="0" label="How many title characters to keep?" help="'0' = keep the whole thing"/>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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43 <param name="keep_first_word" type="boolean" truevalue="id_only" falsevalue="id_and_desc"
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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44 label="Strip fasta description from header?"
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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45 help="Stripping the description will truncate the fasta header to just the sequence ID. Otherwise the header description will be kept. This step is done before the 'How many characters to keep' option."/>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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46 </when>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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47 </conditional>
2
d75972d4bd2a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6e148b31fed1b322ce720804d8525088ec6d43f9
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48
d75972d4bd2a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6e148b31fed1b322ce720804d8525088ec6d43f9
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49 </inputs>
d75972d4bd2a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6e148b31fed1b322ce720804d8525088ec6d43f9
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50 <outputs>
d75972d4bd2a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6e148b31fed1b322ce720804d8525088ec6d43f9
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51 <data name="output" format="tabular"/>
d75972d4bd2a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6e148b31fed1b322ce720804d8525088ec6d43f9
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52 </outputs>
d75972d4bd2a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6e148b31fed1b322ce720804d8525088ec6d43f9
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53 <tests>
d75972d4bd2a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6e148b31fed1b322ce720804d8525088ec6d43f9
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54 <test>
3
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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55 <param name="ref|input" value="454.fasta" />
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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56 <param name="ref|keep_first" value="0"/>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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57 <param name="ref|keep_first_word" value="id_and_desc" />
2
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58 <output name="output" file="fasta_tool_compute_length_1.out" />
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59 </test>
d75972d4bd2a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6e148b31fed1b322ce720804d8525088ec6d43f9
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60
d75972d4bd2a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6e148b31fed1b322ce720804d8525088ec6d43f9
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61 <test>
3
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62 <param name="ref|input" value="extract_genomic_dna_out1.fasta" />
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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63 <param name="ref|keep_first" value="0"/>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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64 <param name="ref|keep_first_word" value="id_and_desc" />
2
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65 <output name="output" file="fasta_tool_compute_length_2.out" />
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66 </test>
d75972d4bd2a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6e148b31fed1b322ce720804d8525088ec6d43f9
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67
d75972d4bd2a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6e148b31fed1b322ce720804d8525088ec6d43f9
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68 <test>
3
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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69 <param name="ref|input" value="454.fasta" />
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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70 <param name="ref|keep_first" value="14"/>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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71 <param name="ref|keep_first_word" value="id_and_desc" />
2
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72 <output name="output" file="fasta_tool_compute_length_3.out" />
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73 </test>
3
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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74
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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75 <test>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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76 <param name="ref|ref_source" value="fasta" />
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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77 <param name="ref|index" value="test_id"/>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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78 <param name="ref|keep_first_word" value="id_only" />
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79 <output name="output" file="merged.tab" />
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80 </test>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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81
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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82 <test>
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83 <param name="ref|ref_source" value="dbkey" />
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84 <param name="ref|index" value="test_id"/>
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85 <output name="output" file="merged.tab" />
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86 </test>
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87 </tests>
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88 <help>
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89
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90 **What it does**
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91
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92 This tool counts the length of each fasta sequence in the file. The output file has two columns per line (separated by tab): fasta titles and lengths of the sequences. The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry.
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93
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94 -----
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95
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96 **Example**
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97
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98 Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run::
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99
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100 &gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
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101 TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG
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102 TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
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103 &gt;EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
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104 AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
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105
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106 Running this tool while setting **How many characters to keep?** to **14** will produce this::
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107
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108 EYKX4VC02EQLO5 108
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109 EYKX4VC02D4GS2 60
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110
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111 However, if your IDs are not all the same length, you may wish to just keep the fasta ID, and not the description::
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112
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113 &gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
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114 TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG
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115 TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
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116 &gt;EYKX4VC length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
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117 AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
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118
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119 Running this tool with **Strip fasta description from header** set to **True** and **How many characters to keep?** set to **0** will produce::
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120
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121 EYKX4VC02EQLO5 108
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122 EYKX4VC 60
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123
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124
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125 </help>
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126 <citations>
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127 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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128 </citations>
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129 </tool>