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