diff obiannotate.xml @ 0:6ddfa9d9653b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/obiannotate.xml	Wed Apr 12 17:37:37 2017 -0400
@@ -0,0 +1,158 @@
+<tool id="obi_annotate" name="obiannotate" version="@WRAPPER_VERSION@">
+    <description>Adds/Edits sequence record annotations</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command>
+
+        <![CDATA[
+        obiannotate
+        ${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
+
+        '$inputseq' > '$output'
+        ]]>
+
+    </command>
+
+    <inputs>
+        <param name="inputseq" type="data" format="fastq,fasta" 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" />
+
+    </inputs>
+    <outputs>
+        <data format="fasta" name="output" label="output.fasta with ${tool.name} on ${on_string}" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="inputseq" value="output_obiuniq.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>
+    </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>