Commit 25e8fd29 authored by Jelle Scholtalbers's avatar Jelle Scholtalbers

use proper input format types in the galaxy wrapper

parent 2594d3fc
...@@ -27,8 +27,8 @@ ...@@ -27,8 +27,8 @@
<xml name="paired_options"> <xml name="paired_options">
<when value="paired"> <when value="paired">
<param name="input_1" format="fastq,gz" type="data" label="FASTQ file #1"/> <param name="input_1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" label="FASTQ file #1"/>
<param name="input_2" format="fastq,gz" type="data" label="FASTQ file #2"/> <param name="input_2" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" label="FASTQ file #2"/>
<yield /> <yield />
<param name="SAME_HEADERS" type="boolean" <param name="SAME_HEADERS" type="boolean"
label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)" label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)"
...@@ -37,7 +37,7 @@ ...@@ -37,7 +37,7 @@
falsevalue="false" checked="false"/> falsevalue="false" checked="false"/>
</when> </when>
<when value="paired_collection"> <when value="paired_collection">
<param name="input_1" format="fastq,gz" type="data_collection" collection_type="paired" <param name="input_1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired"
label="FASTQ Paired Dataset"/> label="FASTQ Paired Dataset"/>
<yield /> <yield />
<param name="SAME_HEADERS" type="boolean" <param name="SAME_HEADERS" type="boolean"
...@@ -70,18 +70,18 @@ ...@@ -70,18 +70,18 @@
<option value="paired_collection">Paired-end Dataset Collection</option> <option value="paired_collection">Paired-end Dataset Collection</option>
</param> </param>
<when value="single"> <when value="single">
<param name="input_1" format="fastq,gz" type="data" label="FASTQ file"/> <param name="input_1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" label="FASTQ file"/>
<param name="I1" type="data" format="fastq,gz" label="First Index File"/> <param name="I1" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="First Index File"/>
</when> </when>
<expand macro="paired_options"> <expand macro="paired_options">
<param name="I1" type="data" format="fastq,gz" label="First Index File"/> <param name="I1" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="First Index File"/>
<conditional name="I2_CONDITIONAL"> <conditional name="I2_CONDITIONAL">
<param name="I2_AVAILABLE" type="select" label="Do you have a second index file?"> <param name="I2_AVAILABLE" type="select" label="Do you have a second index file?">
<option value="true">Yes</option> <option value="true">Yes</option>
<option value="false" selected="true">No</option> <option value="false" selected="true">No</option>
</param> </param>
<when value="true"> <when value="true">
<param name="I2" type="data" format="fastq,gz" label="Second Index File"/> <param name="I2" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="Second Index File"/>
<expand macro="bred_conditional"/> <expand macro="bred_conditional"/>
</when> </when>
<when value="false"/> <when value="false"/>
...@@ -98,7 +98,7 @@ ...@@ -98,7 +98,7 @@
<option value="paired_collection">Paired-end Dataset Collection</option> <option value="paired_collection">Paired-end Dataset Collection</option>
</param> </param>
<when value="single"> <when value="single">
<param name="input_1" format="fastq,gz" type="data" label="FASTQ file"/> <param name="input_1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" label="FASTQ file"/>
</when> </when>
<expand macro="paired_options"> <expand macro="paired_options">
<yield /> <yield />
......
...@@ -4,8 +4,8 @@ Processed Reads (pairs) 25 ...@@ -4,8 +4,8 @@ Processed Reads (pairs) 25
Assigned Reads (pairs) 10 Assigned Reads (pairs) 10
Unassigned Reads (pairs) 15 Unassigned Reads (pairs) 15
# Individual sample read (pair) counts : # Individual sample read (pair) counts :
emb681m1 2
emb681m4 2 emb681m4 2
emb681m5 2 emb681m5 2
emb6801m2 2 emb681m1 2
emb6801m1 2 emb6801m1 2
emb6801m2 2
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