# HG changeset patch
# User iuc
# Date 1710940574 0
# Node ID d50dc96e3ce9e87000d551ab6a684c7742290e8b
# Parent  f82cefbbcea5f1a08650c06bf1f1622a256449d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44

diff -r f82cefbbcea5 -r d50dc96e3ce9 macros.xml
--- 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>
 
diff -r f82cefbbcea5 -r d50dc96e3ce9 obiannotate.xml
--- 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>
diff -r f82cefbbcea5 -r d50dc96e3ce9 test-data/input_ngsfilter_extrafile.txt
--- 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	@