Mercurial > repos > iuc > obi_annotate
changeset 4:d50dc96e3ce9 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
| author | iuc |
|---|---|
| date | Wed, 20 Mar 2024 13:16:14 +0000 |
| parents | f82cefbbcea5 |
| children | |
| files | macros.xml obiannotate.xml test-data/input_ngsfilter_extrafile.txt |
| diffstat | 3 files changed, 185 insertions(+), 180 deletions(-) [+] |
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--- a/macros.xml Mon May 10 19:37:25 2021 +0000 +++ b/macros.xml Wed Mar 20 13:16:14 2024 +0000 @@ -5,7 +5,11 @@ <requirement type="package" version="@TOOL_VERSION@">obitools</requirement> </requirements> </xml> - + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">obitools</xref> + </xrefs> + </xml> <token name="@TOOL_VERSION@">1.2.13</token> <token name="@PROFILE@">21.01</token>
--- a/obiannotate.xml Mon May 10 19:37:25 2021 +0000 +++ b/obiannotate.xml Wed Mar 20 13:16:14 2024 +0000 @@ -1,175 +1,176 @@ -<tool id="obi_annotate" name="obiannotate" version="@TOOL_VERSION@" profile="@PROFILE@"> - <description>Adds/Edits sequence record annotations</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"/> - <expand macro="stdio"/> - <command><![CDATA[ - @GUNZIP_INPUT@ - - obiannotate - --without-progress-bar - ${seqrank} - - #if $rename_tag.old_name and $rename_tag.new_name - -R '$rename_tag.old_name':'$rename_tag.new_name' - #end if - - #if $deletetag_key - --delete-tag='$deletetag_key' - #end if - - #if $set_tag.key and $set_tag.pythonexpression - -S '$set_tag.key':'$set_tag.pythonexpression' - #end if - - #if $taglist - --tag-list='$taglist' - #end if - - #if $setid_pythonexpression - --set-identifier='$setid_pythonexpression' - #end if - - #if $pythonexpression - --run='$pythonexpression' - #end if - - #if $setsequence_pythonexpression - --set-sequence='$setsequence_pythonexpression' - #end if - - #if $setdefinition_pythonexpression - --set-definition='$setdefinition_pythonexpression' - #end if - - #if $key_selector.key - --keep='$key_selector.key' - #end if - #if $key_selector.key2 - --keep='$key_selector.key2' - #end if - #if $key_selector.key3 - --keep='$key_selector.key3' - #end if - #if $key_selector.key4 - --keep='$key_selector.key4' - #end if - #if $key_selector.key5 - --keep='$key_selector.key5' - #end if - - ${length} - ${clearbool} - ${uniqid} - - #if $rankname - --with-taxon-at-rank='$rankname' - #end if - - #if $mclfile - --mcl='$mclfile' - #end if - @INPUT_FORMAT@ - @OUT_FORMAT@ - input - @GZIP_OUTPUT@ - > '$output' - - @GENERATE_GALAXY_JSON@ - ]]></command> - - <inputs> - <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file" /> - <param name="seqrank" type="boolean" label="Add a new attribute seq_rank" truevalue="--seq-rank" falsevalue="" help="Use this option if you want to add a new attribute named seq_rank to the sequence record indicating its entry number in the sequence file" /> - <section name="rename_tag" title="Rename attribute" expanded="False"> - <param name="old_name" type="text" label="old name" optional="true"/> - <param name="new_name" type="text" label="new name" optional="true"/> - </section> - <param name="deletetag_key" type="text" label="Delete attribute" optional="true" help="Use this option if you want to delete attribute named ATTRIBUTE_NAME.When this attribute is missing, the sequence record is skipped and the next one is examined"/> - - <section name="set_tag" title="Create a new attribute" expanded="False"> - <param name="key" type="text" label="key" optional="true"/> - <param name="pythonexpression" type="text" label="python expression" optional="true"/> - </section> - - <param name="taglist" type="data" optional="true" format="txt,tabular" label="Use a tag list" help="file containing identifiers of sequences to select" /> - - <param name="setid_pythonexpression" type="text" label="Set sequence record identifier with a value" help="Use this option if you want to set sequence record identifier with a value computed from PYTHON_EXPRESSION" /> - - <param name="pythonexpression" type="text" label="Run a PYTHON_EXPRESSION on each selected sequence" optional="true" help="Use this option if you want to run a PYTHON_EXPRESSION on each selected sequence"/> - - <param name="setsequence_pythonexpression" type="text" label="Change the sequence itself with a value" help="Use this option if you want to change the sequence itself with a value computed from PYTHON_EXPRESSION"/> - - <param name="setdefinition_pythonexpression" type="text" label="Set sequence definition with a value computed" help="Use this option if you want to set sequence definition with a value computed from PYTHON_EXPRESSION"/> - - <param name="clearbool" type="boolean" label="Clear all attributes associated to the sequence records" truevalue="--clear" falsevalue="" help="Use this option if you want to clear all attributes associated to the sequence records" /> - - <section name="key_selector" title="Keep only attribute with key" expanded="False"> - <param name="key" type="text" label="key" optional="true" /> - <param name="key2" type="text" label="if you want to specify a second key" optional="true" /> - <param name="key3" type="text" label="if you want to specify a third key" optional="true" /> - <param name="key4" type="text" label="if you want to specify a fourth key" optional="true" /> - <param name="key5" type="text" label="if you want to specify a fifth key" optional="true" /> - </section> - - <param name="length" type="boolean" label="Use the length option?" truevalue="--length" falsevalue="" help="Use this option if you want to add attribute with seq_length as a key and sequence length as a value" /> - - <param name="rankname" type="text" label="Add taxonomic annotation" help="Use this option if you want to add taxonomic annotation at taxonomic rank RANK_NAME"/> - - <param name="mclfile" optional="true" type="data" format="txt,tabular" label="mcl file" help="use this option if you want to add a new attribute containing the number of the cluster the sequence record was assigned to, as indicated in file MCLFILE" /> - - <param name="uniqid" type="boolean" label="Force sequence record ids to be unique" truevalue="--uniq-id" falsevalue="" help="Use this option if you want to force sequence record ids to be unique" /> - <expand macro="input_format_options_macro"/> - <expand macro="out_format_macro"/> - </inputs> - <outputs> - <data name="output" format="auto"/> - </outputs> - <tests> - <test> - <param name="input" value="output_obiuniq.fasta" ftype="fasta"/> - <section name="key_selector"> - <param name="key" value="count" /> - <param name="key2" value="merged_sample" /> - </section> - <param name="uniqid" value="true" /> - <param name="clearbool" value="true" /> - <param name="length" value="true" /> - <param name="seqrank" value="true" /> - - <output name="output" file="output_obiannotate.fasta" ftype="fasta"/> - </test> - <test> - <param name="input" value="output_obiuniq.fasta.gz" ftype="fasta.gz"/> - <section name="key_selector"> - <param name="key" value="count" /> - <param name="key2" value="merged_sample" /> - </section> - <param name="uniqid" value="true" /> - <param name="clearbool" value="true" /> - <param name="length" value="true" /> - <param name="seqrank" value="true" /> - <output name="output" file="output_obiannotate.fasta.gz" ftype="fasta.gz" decompress="true"/> - </test> - <!-- TODO fastq input test --> - </tests> - - <help><![CDATA[ - -.. class:: infomark - -**What it does** - -`obiannotate` is the command that allows adding/modifying/removing annotation attributes attached to sequence records. - -Once such attributes are added, they can be used by the other OBITools commands for filtering purposes or for statistics computing. - -@OBITOOLS_LINK@ - -]]> - - </help> - <expand macro="citation" /> -</tool> +<tool id="obi_annotate" name="obiannotate" version="@TOOL_VERSION@" profile="@PROFILE@"> + <description>Adds/Edits sequence record annotations</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="bio_tools"/> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command><![CDATA[ + @GUNZIP_INPUT@ + + obiannotate + --without-progress-bar + ${seqrank} + + #if $rename_tag.old_name and $rename_tag.new_name + -R '$rename_tag.old_name':'$rename_tag.new_name' + #end if + + #if $deletetag_key + --delete-tag='$deletetag_key' + #end if + + #if $set_tag.key and $set_tag.pythonexpression + -S '$set_tag.key':'$set_tag.pythonexpression' + #end if + + #if $taglist + --tag-list='$taglist' + #end if + + #if $setid_pythonexpression + --set-identifier='$setid_pythonexpression' + #end if + + #if $pythonexpression + --run='$pythonexpression' + #end if + + #if $setsequence_pythonexpression + --set-sequence='$setsequence_pythonexpression' + #end if + + #if $setdefinition_pythonexpression + --set-definition='$setdefinition_pythonexpression' + #end if + + #if $key_selector.key + --keep='$key_selector.key' + #end if + #if $key_selector.key2 + --keep='$key_selector.key2' + #end if + #if $key_selector.key3 + --keep='$key_selector.key3' + #end if + #if $key_selector.key4 + --keep='$key_selector.key4' + #end if + #if $key_selector.key5 + --keep='$key_selector.key5' + #end if + + ${length} + ${clearbool} + ${uniqid} + + #if $rankname + --with-taxon-at-rank='$rankname' + #end if + + #if $mclfile + --mcl='$mclfile' + #end if + @INPUT_FORMAT@ + @OUT_FORMAT@ + input + @GZIP_OUTPUT@ + > '$output' + + @GENERATE_GALAXY_JSON@ + ]]></command> + + <inputs> + <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file" /> + <param name="seqrank" type="boolean" label="Add a new attribute seq_rank" truevalue="--seq-rank" falsevalue="" help="Use this option if you want to add a new attribute named seq_rank to the sequence record indicating its entry number in the sequence file" /> + <section name="rename_tag" title="Rename attribute" expanded="False"> + <param name="old_name" type="text" label="old name" optional="true"/> + <param name="new_name" type="text" label="new name" optional="true"/> + </section> + <param name="deletetag_key" type="text" label="Delete attribute" optional="true" help="Use this option if you want to delete attribute named ATTRIBUTE_NAME.When this attribute is missing, the sequence record is skipped and the next one is examined"/> + + <section name="set_tag" title="Create a new attribute" expanded="False"> + <param name="key" type="text" label="key" optional="true"/> + <param name="pythonexpression" type="text" label="python expression" optional="true"/> + </section> + + <param name="taglist" type="data" optional="true" format="txt,tabular" label="Use a tag list" help="file containing identifiers of sequences to select" /> + + <param name="setid_pythonexpression" type="text" label="Set sequence record identifier with a value" help="Use this option if you want to set sequence record identifier with a value computed from PYTHON_EXPRESSION" /> + + <param name="pythonexpression" type="text" label="Run a PYTHON_EXPRESSION on each selected sequence" optional="true" help="Use this option if you want to run a PYTHON_EXPRESSION on each selected sequence"/> + + <param name="setsequence_pythonexpression" type="text" label="Change the sequence itself with a value" help="Use this option if you want to change the sequence itself with a value computed from PYTHON_EXPRESSION"/> + + <param name="setdefinition_pythonexpression" type="text" label="Set sequence definition with a value computed" help="Use this option if you want to set sequence definition with a value computed from PYTHON_EXPRESSION"/> + + <param name="clearbool" type="boolean" label="Clear all attributes associated to the sequence records" truevalue="--clear" falsevalue="" help="Use this option if you want to clear all attributes associated to the sequence records" /> + + <section name="key_selector" title="Keep only attribute with key" expanded="False"> + <param name="key" type="text" label="key" optional="true" /> + <param name="key2" type="text" label="if you want to specify a second key" optional="true" /> + <param name="key3" type="text" label="if you want to specify a third key" optional="true" /> + <param name="key4" type="text" label="if you want to specify a fourth key" optional="true" /> + <param name="key5" type="text" label="if you want to specify a fifth key" optional="true" /> + </section> + + <param name="length" type="boolean" label="Use the length option?" truevalue="--length" falsevalue="" help="Use this option if you want to add attribute with seq_length as a key and sequence length as a value" /> + + <param name="rankname" type="text" label="Add taxonomic annotation" help="Use this option if you want to add taxonomic annotation at taxonomic rank RANK_NAME"/> + + <param name="mclfile" optional="true" type="data" format="txt,tabular" label="mcl file" help="use this option if you want to add a new attribute containing the number of the cluster the sequence record was assigned to, as indicated in file MCLFILE" /> + + <param name="uniqid" type="boolean" label="Force sequence record ids to be unique" truevalue="--uniq-id" falsevalue="" help="Use this option if you want to force sequence record ids to be unique" /> + <expand macro="input_format_options_macro"/> + <expand macro="out_format_macro"/> + </inputs> + <outputs> + <data name="output" format="auto"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input" value="output_obiuniq.fasta" ftype="fasta"/> + <section name="key_selector"> + <param name="key" value="count"/> + <param name="key2" value="merged_sample"/> + </section> + <param name="uniqid" value="true"/> + <param name="clearbool" value="true"/> + <param name="length" value="true"/> + <param name="seqrank" value="true"/> + + <output name="output" file="output_obiannotate.fasta" ftype="fasta"/> + </test> + <test expect_num_outputs="1"> + <param name="input" value="output_obiuniq.fasta.gz" ftype="fasta.gz"/> + <section name="key_selector"> + <param name="key" value="count"/> + <param name="key2" value="merged_sample"/> + </section> + <param name="uniqid" value="true"/> + <param name="clearbool" value="true"/> + <param name="length" value="true"/> + <param name="seqrank" value="true"/> + <output name="output" file="output_obiannotate.fasta.gz" ftype="fasta.gz" decompress="true"/> + </test> + <!-- TODO fastq input test --> + </tests> + + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +`obiannotate` is the command that allows adding/modifying/removing annotation attributes attached to sequence records. + +Once such attributes are added, they can be used by the other OBITools commands for filtering purposes or for statistics computing. + +@OBITOOLS_LINK@ + +]]> + + </help> + <expand macro="citation" /> +</tool>
--- a/test-data/input_ngsfilter_extrafile.txt Mon May 10 19:37:25 2021 +0000 +++ b/test-data/input_ngsfilter_extrafile.txt Wed Mar 20 13:16:14 2024 +0000 @@ -1,4 +1,4 @@ -wolf_diet 13a_F730603 aattaac TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ -wolf_diet 15a_F730814 gaagtag TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ -wolf_diet 26a_F040644 gaatatc TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ -wolf_diet 29a_F260619 gcctcct TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ +wolf_diet 13a_F730603 aattaac TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ +wolf_diet 15a_F730814 gaagtag TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ +wolf_diet 26a_F040644 gaatatc TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ +wolf_diet 29a_F260619 gcctcct TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @