diff daa2info.xml @ 0:2f8df8e575f2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/daa2info.xml	Fri Dec 03 23:09:26 2021 +0000
@@ -0,0 +1,143 @@
+<tool id="megan_daa2info" name="MEGAN: Get information" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>about a DIAMOND file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+#set input_identifier = 'input.' + $input.ext.upper()
+ln -s '${input}' '${input_identifier}' &&
+
+daa2info 
+--in '${input_identifier}'
+#if str($input_is_meganized_cond.input_is_meganized) == 'yes':
+    --listMore
+    #if str($input_is_meganized_cond.list_class2count_cond.list_class2count) == 'yes':
+        --class2count '$input_is_meganized_cond.list_class2count_cond.class2count'
+        $input_is_meganized_cond.list_class2count_cond.sum
+    #end if
+    #if str($input_is_meganized_cond.list_read2class_cond.list_read2class) == 'yes':
+        --read2class '$input_is_meganized_cond.list_read2class_cond.read2class'
+    #end if
+    $input_is_meganized_cond.names
+    $input_is_meganized_cond.paths
+    $input_is_meganized_cond.prefixRank
+    $input_is_meganized_cond.majorRanksOnly
+    #if str($input_is_meganized_cond.bo_or_vo) != 'do_not_restrict':
+        $input_is_meganized_cond.bo_or_vo
+    #end if
+    $input_is_meganized_cond.ignoreUnassigned
+#else:
+    --list
+#end if
+#if $extractSummaryFile:
+    --extractSummaryFile '$output_summary'
+#end if
+--out '${output}'
+]]></command>
+    <inputs>
+        <param name="input" argument="--in" type="data" format="daa" label="Input DIAMOND file"/>
+        <conditional name="input_is_meganized_cond">
+            <param name="input_is_meganized" type="select" checked="false" label="Input is meganized?" help="Implies the input file was produced by the MEGAN: DAA Meganizer tool">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+                <conditional name="list_class2count_cond">
+                    <param name="list_class2count" type="select" label="List class to count for named classification(s)?">
+                        <option value="no" selected="true">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no"/>
+                    <when value="yes">
+                        <param argument="--class2count" type="select" label="Select class to count for named classification(s)">
+                            <expand macro="classification_options"/>
+                        </param>
+                        <param argument="--sum" type="boolean" truevalue="--sum" falsevalue="" checked="false" label="Use summarized rather than assigned counts when listing class to count?"/>
+                    </when>
+                </conditional>
+                <conditional name="list_read2class_cond">
+                    <param name="list_read2class" type="boolean" truevalue="true" falsevalue="false" checked="false" label="List read to class assignments for named classification(s)?"/>
+                    <when value="false"/>
+                    <when value="true">
+                        <param argument="--read2class" type="select" label="Select read to class assignments for named classification(s)">
+                            <expand macro="classification_options"/>
+                        </param>
+                    </when>
+                </conditional>
+                <param argument="--names" type="boolean" truevalue="--names" falsevalue="" checked="false" label="Report class names rather than class Id numbers?"/>
+                <param argument="--paths" type="boolean" truevalue="--paths" falsevalue="" checked="false" label="Report class paths rather than class Id numbers?"/>
+                <param argument="--prefixRank" type="boolean" truevalue="--prefixRank" falsevalue="" checked="false" label="When reporting class paths for taxonomy, prefix single letter to indicate taxonomic rank?"/>
+                <param argument="--majorRanksOnly" type="boolean" truevalue="--majorRanksOnly" falsevalue="" checked="false" label="Only use major taxonomic ranks?"/>
+                <param name="bo_or_vo" type="select" label="Restrict reporting to either bacterial reads or viral reads in taxonomic report">
+                    <option value="do_not_restrict" selected="true">Do not restrict</option>
+                    <option value="--bacteriaOnly" selected="true">Bacterial reads and counts</option>
+                    <option value="--virusOnly">Viral reads and counts</option>
+                </param>
+                <param argument="--ignoreUnassigned" type="boolean" truevalue="--ignoreUnassigned" falsevalue="" checked="true" label="Don't report on reads that are unassigned?"/>
+            </when>
+        </conditional>
+        <param argument="--extractSummaryFile" type="boolean" truevalue="--extractSummaryFile" falsevalue="" checked="false" label="Output a MEGAN summary file?" help="Contains all classifications, but no reads or alignments"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt"/>
+        <data name="output_summary" format="txt" label="${tool.name} on ${on_string} (MEGAN summary)">
+            <filter>extractSummaryFile</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="input.daa" ftype="daa"/>
+            <output name="output" file="daa2info_output1.txt" ftype="txt" compare="contains"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="input_meganized.daa" ftype="daa"/>
+            <param name="input_is_meganized" value="yes"/>
+            <output name="output" file="daa2info_output2.txt" ftype="txt" compare="contains"/>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="input" value="input_meganized.daa" ftype="daa"/>
+            <param name="input_is_meganized" value="yes"/>
+            <param name="bo_or_vo" value="--virusOnly"/>
+            <param name="extractSummaryFile" value="true"/>
+            <output name="output" file="daa2info_output2.txt" ftype="txt" compare="contains"/>
+            <output name="output_summary" file="daa2info_output_summary2.txt" ftype="txt" compare="contains"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Analyses a DIAMOND (i.e., a Direct Access Archive or DAA) file, a proprietary file format developed by PowerISO Computing
+for disk image files, and outputs a text file containing information about the file.  The information includes the following.
+
+ * Number of reads
+ * Alignment mode
+ * Whether the file is meganized
+ * Classifications
+
+If the DIAMOND file is meganized (i.e., it was produced by the MEGAN: DAA Meganizer tool), a summary that includes the
+following information (among other items) is included in the output.
+
+ * Content type
+ * Names
+ * Uids
+ * Sizes
+ * Additional reads
+ * Algorithm
+ * Parameters
+
+If the user elects to output a MEGAN summary file, an additional text file that includes the following information (among
+other items) is produced.
+
+ * Creator
+ * Creation date
+ * Content type
+ * Blast mode
+ * Uids
+
+    </help>
+    <expand macro="citations"/>
+</tool>
+