--- a/seqsero.xml.txt	Thu Sep 05 10:02:01 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,175 +0,0 @@
-<tool id="seqsero2_v1_0_1" name="SeqSero 2" version="1.0.1">
-    <description>Salmonella serotype prediction</description>
-    <requirements>
-      <requirement type="package" version="3.6">python</requirement>
-      <requirement type="package" version="1.73">biopython</requirement>
-      <requirement type="package" version="2.7.1">blast</requirement>
-      <requirement type="package" version="1.9">samtools</requirement>
-      <requirement type="package" version="2.9.1">sra-tools</requirement>
-      <requirement type="package" version="0.7.17">bwa</requirement>
-      <requirement type="package" version="3.13.1">spades</requirement>
-      <requirement type="package" version="2.27.1">bedtools</requirement>
-      <requirement type="package">salmid</requirement>
-    </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-      echo "SeqSero 2 v. 1.0.1" ;
-      #if $reads.reads_select == 'history'
-      #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
-      #set $forward = $reads.forward
-      #set $reverse = $reads.reverse
-      #else
-      #set $name = $reads.coll.name.replace(' ', '_')
-      #set $forward = $reads.coll.forward
-      #set $reverse = $reads.coll.reverse
-      #end if
-        echo $name ;
-        echo "-=-=-=-=-" ;
-      #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
-        gunzip -c $forward > forward.fastq;
-      #set $forward = './forward.fastq'
-      #end if
-      #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
-        gunzip -c $reverse > reverse.fastq;
-      #set $reverse = './reverse.fastq'
-      #end if
-        ln -s $forward ${name}_1.fastq;
-        ln -s $reverse ${name}_2.fastq;
-        mkdir ./output;
-        touch output/SeqSero_log.txt ;
-        python $__tool_directory__/SeqSero2_package.py
-        -p \${GALAXY_SLOTS:-4}
-        -t 2
-        -m $mode
-        -d ./output
-      #if $mode == 'a':
-        -b $maptype 
-      #end if
-        -i ${name}_1.fastq ${name}_2.fastq &&
-        echo "-=-=-=-=-" &&
-        cat output/SeqSero_log.txt &&
-        echo "-=-=-=-=-" &&
-        ls -lah ./output
-    ]]></command>
-    <inputs>
-        
-        <conditional name="reads">
-            <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
-                <option value="collection">Paired collection from your history</option>
-                <option value="history">Two FASTQ datasets from your history</option>
-            </param>
-            <when value="collection">
-                <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
-            </when>
-            <when value="history">
-                <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
-                <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
-            </when>
-        </conditional>
-     
-          <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
-          <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
-          <!-- <param name="numofthr" type="select" label="Number of threads">
-          <option value="1">1</option>
-          <option value="2">2</option>
-          <option value="3">3</option>
-          <option value="4">4</option> -->
-        <!-- </param> -->
-        
-        <param label="Analysis mode" type="select" name="mode">
-         <option value="a">allele mode</option>
-            <option value="k">k-mer mode</option>
-        </param>
-
-        <param name="maptype" type="select" label="Algorithms for BWA mapping">
-          <option value="mem">mem</option>
-          <option value="sam">sam</option>
-        </param>
-
-    
-
-    </inputs>
-    <outputs>
-      <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/Seqsero_result.tsv"/>
-    </outputs>
-    <tests>
-       <!-- <test>
-         <param name="reads_select" value="history" />
-         <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
-         <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
-         <output name="results" file="Seqsero_result.tsv" />
-       </test>
-       <test>
-        <param name="reads_select" value="collection" />
-        <param name="coll">
-            <collection type="paired">
-                <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
-                <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
-            </collection>
-        </param>
-        <output name="results" file="Seqsero_result.tsv" />
-       </test> -->
-        <test>
-         <param name="mode" value="k" />
-         <param name="reads_select" value="history" />
-         <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
-         <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
-         <output name="results" file="Seqsero_result_25k.tsv" />
-       </test>
-       <test>
-        <param name="mode" value="k" />
-        <param name="reads_select" value="collection" />
-        <param name="coll">
-            <collection type="paired">
-                <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
-                <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
-            </collection>
-        </param>
-        <output name="results" file="Seqsero_result_25k_coll.tsv" />
-       </test>
-        <test>
-         <param name="mode" value="a" />
-         <param name="reads_select" value="history" />
-         <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
-         <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
-         <assert_stdout>
-          <has_text text="predicted antigenic profile does not exist" />
-         </assert_stdout>
-       </test>
-       <!-- <test>
-        <param name="mode" value="a" />
-        <param name="reads_select" value="collection" />
-        <param name="coll">
-            <collection type="paired">
-                <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
-                <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
-            </collection>
-        </param>
-        <output name="results" file="Seqsero_result_allele.tsv" />
-       </test> -->
-    </tests>
-    <help><![CDATA[
-    
-**Usage: SeqSero2.py** 
-
-**Algorithms for BWA mapping**
-
-'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
-   
-    ]]></help>
-    <citations>
-       <citation type="bibtex">
-        @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
-        title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
-        journal={J Clin Microbiol}, publisher={ASM},
-        author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
-        year={2015}, month={Max},
-        url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
-       }</citation>
-       <citation type="bibtex">
-        @misc{cfsan_biostatistics_group_2017,
-        title={CFSAN Biostatistics Group fork of SeqSero2},
-        url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},
-       </citation>
-    </citations>
-
-</tool>
\ No newline at end of file