diff vsnp_sample_names.xml @ 0:f75e2ac7b6cd draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vsnp_sample_names.xml	Tue Apr 21 10:17:20 2020 -0400
@@ -0,0 +1,91 @@
+<tool id="vsnp_sample_names" name="vSNP: sample names" version="1.0.0">
+    <description></description>
+    <command detect_errors="exit_code"><![CDATA[
+#import os
+#import re
+#set output_dir = 'output'
+mkdir -p $output_dir
+#if str($input_type_cond.input_type) == "single":
+    ## We may have a single read or a pair, but in
+    ## either case we want the same base file name.
+    #set sample_name = $os.path.basename($input_type_cond.read.element_identifier)
+    #if $sample_name.find(".") > 0:
+        #set sample_name = $sample_name.split(".")[0]
+    #end if
+    #if $sample_name.find("_") > 0:
+        #set sample_name = $sample_name.split("_")[0]
+    #end if
+    echo $sample_name > $output
+#else:
+    #for $i in $input_type_cond.reads_collection:
+        #set sample_name = $os.path.basename($i.element_identifier)
+        #if $sample_name.find(".") > 0:
+            #set sample_name = $sample_name.split(".")[0]
+        #end if
+        #set output_file = $os.path.join($output_dir, $sample_name)
+        && echo $sample_name > $output_file
+    #end for
+#end if
+]]></command>
+    <inputs>
+        <conditional name="input_type_cond">
+            <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
+                <option value="single" selected="true">Single files</option>
+                <option value="collection">Collections of files</option>
+            </param>
+            <when value="single">
+                <param name="read" type="data" format="fastqsanger.gz,fastqsanger" label="Sample file"/>
+            </when>
+            <when value="collection">
+                <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="list" label="Collection of sample files"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt">
+            <filter>input_type_cond['input_type'] == 'single'</filter>
+        </data>
+        <collection name="output__collection" type="list">
+            <discover_datasets pattern="__name__" directory="output" format="txt" />
+            <filter>input_type_cond['input_type'] == 'collection'</filter>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_type" value="collection"/>
+            <param name="reads_collection">
+                <collection type="list">
+                    <element name="BCG_Danish_Human_UK_SRR9596061.fastq" value="BCG_Danish_Human_UK_SRR9596061.fastq" dbkey="89"/>
+                    <element name="Dassie_Dassie_ZA_SRR3745455.fastq" value="Dassie_Dassie_ZA_SRR3745455.fastq" dbkey="89"/>
+                    <element name="Mbov_Cattle_NI_SRR10993937.fastq" value="Mbov_Cattle_NI_SRR10993937.fastq" dbkey="89"/>
+                </collection>
+            </param>
+            <output_collection name="output__collection" type="list">
+                <element name="BCG_Danish_Human_UK_SRR9596061" file="BCG_Danish_Human_UK_SRR9596061" ftype="txt"/>
+                <element name="Dassie_Dassie_ZA_SRR3745455" file="Dassie_Dassie_ZA_SRR3745455" ftype="txt"/>
+                <element name="Mbov_Cattle_NI_SRR10993937" file="Mbov_Cattle_NI_SRR10993937" ftype="txt"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Accepts one or more sample files and extracts a unique portion of the file name as the content of the output file(s).  These
+text files are then used as workflow parameter values for the Read Group Identifier parameter in the bwa-mem tool.
+
+**Required Options**
+
+ * **Choose the category of the files to be analyzed** - select "Single files" or "Collections of files", then select the appropriate history items (single or paired fastqsanger reads or collections of fastqsanger reads) based on the selected option.
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @misc{None,
+            journal = {None},
+            author = {1. Stuber T},
+            title = {Manuscript in preparation},
+            year = {None},
+            url = {https://github.com/USDA-VS/vSNP},}
+        </citation>
+    </citations>
+</tool>
+