changeset 3:69d3e3d80de6 draft

Deleted selected files

--- a/biotradis_bacteria_tradis.xml	Thu Jul 25 05:50:27 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,93 +0,0 @@
-<tool id="add_tradis_tags" name="add tradis tags" version="@VERSION@">
-    <description>Generates a BAM file with tags added to read strings.</description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <command detect_errors="exit_code"><![CDATA[
-        #import re
-
-        ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
-        ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
-        #set $named_input_files = ''
-        #for $input_file in $input_files
-            ## Add single quotes around each input file identifier
-            #set $_input_file = "'{}'".format($input_file.element_identifier)
-            ln -s '${input_file}' ${_input_file} &&
-            echo ${_input_file} >> fq.list &&
-        #end for
-
-        bacteria_tradis -f fq.list
-                        -t $tag
-                        -r $ref
-                        -td $tag_dir
-                        -mm $mm
-                        -m $m
-                    #if str($smalt_k)!=""
-                        --smalt_k $smalt_k
-                    #end if
-                    #if str($smalt_s)!=""
-                        --smalt_s $smalt_s
-                    #end if
-                        --smalt_y $smalt_y
-                        --smalt_r $smalt_r
-                        -n "\${GALAXY_SLOTS:-2}"
-                    #if $verbose
-                        --verbose
-                    #end if
-                    && tar cvzf insert_site_plot.tar.gz *insert_site_plot.gz
-                    && tar cvzf mapped.tar.gz *mapped.bam*
-    ]]></command>
-    <inputs>
-        <param name="input_files" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" multiple="true" />
-        <param name="tag" type="text" label="Tag" help="Tag to search for" />
-        <param name="ref" type="data" format="fasta" label="Reference geome" help="Fasta format" />
-        <param name="tag_dir" type="select" label="Tag direction" help="3 or 5(optional. default = 3)" >
-            <option value="3" selected="true">3</option>
-            <option value="5">5</option>
-        </param>
-        <param name="mm" type="integer" value="0" label="Number of mismatches allowed when matching tag" help="(optional. default = 0)" />
-        <param name="m" type="integer" value="30" label="Mapping quality cutoff score" help="(optional. default = 30)" />
-        <param argument="--smalt_k" type="integer" value="" optional="True" label="Custom k-mer value for SMALT mapping" help="(optional)" />
-        <param argument="--smalt_s" type="integer" value="" optional="True" label="Custom step size for SMALT mapping" help="(optional)" />
-        <param argument="--smalt_y" type="integer" value="0.96" label="Custom y parameter for SMALT" help="(optional. default = 0.96)" />
-        <param argument="--smalt_r" type="integer" value="-1" label="custom r parameter for SMALT" help="(optional. default = -1)" />
-        <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" />
-    </inputs>
-
-    <outputs>
-        <data name="insert_size_plots" format="tar.gz" label="${tool.name} on ${on_string}: Insert size plot" from_work_dir="insert_site_plot.tar.gz"/>
-        <data name="mapped_bam" format="tar.gz" label="${tool.name} on ${on_string}: Insert size plot" from_work_dir="mapped.tar.gz"/>   
-        <data name="fastq_stats" format="txt" label="${tool.name} on ${on_string}: Fastq Stats" from_work_dir="fastqs.stats"/> 
-    </outputs>
-  
-    <help>
-    <![CDATA[
-        Run a TraDIS analysis. This involves:
-        1: filtering the data with tags matching that passed via -t option
-        2: removing the tags from the sequences
-        3: mapping
-        4: creating an insertion site plot
-        5: creating a stats summary
-
-        Usage: bacteria_tradis [options]
-
-        Options:
-        -f        : text file listing fastq files with tradis tags attached
-        -t        : tag to search for
-        -r        : reference genome in fasta format (.fa)
-        -td       : tag direction - 3 or 5 (optional. default = 3)
-        -mm       : number of mismatches allowed when matching tag (optional. default = 0)
-        -m        : mapping quality cutoff score (optional. default = 30)
-        --smalt_k : custom k-mer value for SMALT mapping (optional)
-        --smalt_s : custom step size for SMALT mapping (optional)
-        --smalt_y : custom y parameter for SMALT (optional. default = 0.96)
-        --smalt_r : custom r parameter for SMALT (optional. default = -1)
-        -n        : number of threads to use for SMALT and samtools sort (optional. default = 1)
-        -e        : set defaults for essentiality experiment (smalt_r = 0, -m = 0)
-        -v        : verbose debugging output
-
-        Documentation can be found at `site <https://github.com/sanger-pathogens/Bio-Tradis>`_.
-    ]]></help>
-
-</tool>