# HG changeset patch
# User bgruening
# Date 1390328073 18000
# Node ID da0a1fcf7fe0deb3250e97e922b92525812cab7e
# Parent  97449a3c1f27f8d04bb8de717a97e7e0a67af325
Uploaded

diff -r 97449a3c1f27 -r da0a1fcf7fe0 macs2_bdgbroadcall.xml
--- a/macs2_bdgbroadcall.xml	Tue Jan 21 11:50:01 2014 -0500
+++ b/macs2_bdgbroadcall.xml	Tue Jan 21 13:14:33 2014 -0500
@@ -6,7 +6,6 @@
         <import>macs2_macros.xml</import>
     </macros>
     <command>
-
         macs2 bdgbroadcall
             --ifile $infile
             --cutoff-peak $cutoffpeak
@@ -15,17 +14,15 @@
             --lvl1-max-gap $LVL1MAXGAP
             --lvl2-max-gap $LVL2MAXGAP
             --ofile $ofile
-
     </command>
+    <expand macro="stdio" />
     <inputs>
-
         <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" />
         <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0" help="depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 2 means qvalue 0.01. DEFAULT: 2.0 (--cutoff-peak)"/>
         <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0" help="Cutoff for linking regions/low abundance regions depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 1 means qvalue 0.1, and score 0.3 means qvalue 0.5. DEFAULT: 1 (--cutoff-link)"/>
         <param name="minlen" type="integer" label="Minimum length of peak" value="200" help="better to set it as d value" />
         <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30" help="better to set it as tag size" />
         <param name="LVL2MAXGAP" type="integer" label="Maximum linking between significant peaks" value="800" help="better to set it as 4 times of d value" />
-
     </inputs>
 
     <outputs>
diff -r 97449a3c1f27 -r da0a1fcf7fe0 macs2_bdgcmp.xml
--- a/macs2_bdgcmp.xml	Tue Jan 21 11:50:01 2014 -0500
+++ b/macs2_bdgcmp.xml	Tue Jan 21 13:14:33 2014 -0500
@@ -17,6 +17,7 @@
             --ofile $ofile
 
     </command>
+    <expand macro="stdio" />
     <inputs>
     <!--experiment name and option of selecting paired or single end will always be present-->
     <param name="experiment_name" type="text" value="MACS2 in Galaxy" size="50" label="Experiment Name"/>
diff -r 97449a3c1f27 -r da0a1fcf7fe0 macs2_bdgdiff.xml
--- a/macs2_bdgdiff.xml	Tue Jan 21 11:50:01 2014 -0500
+++ b/macs2_bdgdiff.xml	Tue Jan 21 13:14:33 2014 -0500
@@ -29,6 +29,7 @@
                 --ofile-both-conditions $output_both
             #end if
     </command>
+    <expand macro="stdio" />
     <inputs>
         <param name="infile_pileup_cond1" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 1" />
         <param name="infile_pileup_cond2" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 2" />
diff -r 97449a3c1f27 -r da0a1fcf7fe0 macs2_bdgpeakcall.xml
--- a/macs2_bdgpeakcall.xml	Tue Jan 21 11:50:01 2014 -0500
+++ b/macs2_bdgpeakcall.xml	Tue Jan 21 13:14:33 2014 -0500
@@ -6,7 +6,6 @@
         <import>macs2_macros.xml</import>
     </macros>
     <command>
-
         macs2 bdgpeakcall
         --ifile $infile
         --cutoff $cutoff
@@ -15,8 +14,8 @@
         $callsummits
         $notrackline
         --ofile $ofile
-
     </command>
+    <expand macro="stdio" />
     <inputs>
         <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" />
 
diff -r 97449a3c1f27 -r da0a1fcf7fe0 macs2_callpeak.xml
--- a/macs2_callpeak.xml	Tue Jan 21 11:50:01 2014 -0500
+++ b/macs2_callpeak.xml	Tue Jan 21 13:14:33 2014 -0500
@@ -33,16 +33,12 @@
             $advanced_options.nolambda
 
             #if str($advanced_options.broad_options.broad_options_selector) == '--broad':
-                #set $__options['broad'] = str( $advanced_options.broad_options.broad_options_selector )
-                #set $__options['broad_cutoff'] = float( str( $advanced_options.broad_options.broad_cutoff ) )
-            #end if
-
-            #if str($advanced_options.broad_options.broad_options_selector) == '--broad':
                 --broad
                 --broad-cutoff='$advanced_options.broad_options.broad_cutoff'
             #end if
 
         #else:
+            ## set default parameter
             --mfold 10 30
         #end if
 
@@ -114,6 +110,7 @@
 
         cat $temp_stderr 2>&#38;1
     </command>
+    <expand macro="stdio" />
     <inputs>
         <param name="input_control_file" type="data" format="bam,sam,bed" multiple="True" optional="True" label="ChIP-Seq Control File" />
         <param name="input_treatment_file" type="data" format="bam,sam,bed" multiple="True" label="ChIP-Seq Treatment File" />
diff -r 97449a3c1f27 -r da0a1fcf7fe0 macs2_filterdup.xml
--- a/macs2_filterdup.xml	Tue Jan 21 11:50:01 2014 -0500
+++ b/macs2_filterdup.xml	Tue Jan 21 13:14:33 2014 -0500
@@ -20,6 +20,7 @@
             --keep-dup str( $keep_dup_options.keep_dup_options_selector )
         #end if
     </command>
+    <expand macro="stdio" />
     <inputs>
 
         <!--may need to add a few more formats at later time-->
diff -r 97449a3c1f27 -r da0a1fcf7fe0 macs2_predict.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macs2_predict.xml	Tue Jan 21 13:14:33 2014 -0500
@@ -0,0 +1,66 @@
+<tool id="macs2_predict" name="Predict" version="2.0.10.0">
+    <description>d or fragment size from alignment results</description>
+    <expand macro="requirements">
+        <requirement type="package" version="3.0.1">R_3_0_1</requirement>
+    </expand>
+    <expand macro="version_command" />
+    <macros>
+        <import>macs2_macros.xml</import>
+    </macros>
+    <command>
+        macs2 predict
+            -i #echo ','.join($infiles)#
+            --tsize $tsize
+            @effective_genome_size@
+            --bw $band_width
+            --mfold $advanced_options.mfoldlo $advanced_options.mfoldhi
+            &gt; $outfile;
+
+        Rscript predicted_model.R &gt; $outfile_image
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <repeat name="infiles" title="ChIP-seq alignment files" min="1" 
+            help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command.">
+
+            <param name="infile" type="data" format="bam,sam,bed" multiple="True" optional="True" label="ChIP-seq alignment file" help="-i" />
+        </repeat>
+
+        <expand macro="conditional_effective_genome_size" />
+        <expand macro="tag_size" />
+
+        <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size"
+            help="This value is only used while building the shifting model. (--bw)" />
+
+        <param name="mfoldlo" type="integer" label="Fold-enrichment lower limit" value="5"
+            help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
+        <param name="mfoldhi" type="integer" label="Fold-enrichment upper-limit" value="50"
+            help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
+
+    </inputs>
+
+    <outputs>
+        <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" />
+        <data name="outfile_image" format="png" label="${tool.name} on ${on_string} - X-correlation image" />
+    </outputs>
+    <tests>
+        <!--none yet for macs2-->
+    </tests>
+    <help>
+**What it does**
+
+bdgdiff from macs2
+
+
+Note that pair-end data is not supposed to work with this command.
+
+
+------
+
+**Citation**
+
+For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
+
+Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
+    </help>
+</tool>
diff -r 97449a3c1f27 -r da0a1fcf7fe0 macs2_randsample.xml
--- a/macs2_randsample.xml	Tue Jan 21 11:50:01 2014 -0500
+++ b/macs2_randsample.xml	Tue Jan 21 13:14:33 2014 -0500
@@ -18,8 +18,8 @@
         #else:
             $method_options.number
         #end if
-
     </command>
+    <expand macro="stdio" />
     <inputs>
 
         <!--may need to add a few more formats at later time-->
diff -r 97449a3c1f27 -r da0a1fcf7fe0 macs2_refinepeak.xml
--- a/macs2_refinepeak.xml	Tue Jan 21 11:50:01 2014 -0500
+++ b/macs2_refinepeak.xml	Tue Jan 21 13:14:33 2014 -0500
@@ -6,7 +6,6 @@
         <import>macs2_macros.xml</import>
     </macros>
     <command>
-
         macs2 refinepeak
             -b $bed_infile
             -i $infile
@@ -14,8 +13,8 @@
             --cutoff $cutoff
             --window-size $winsize
             --ofile $ofile
-
     </command>
+    <expand macro="stdio" />
     <inputs>
         <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
         <param name="bed_infile" type="data" format="bed" label="Candidate peak file in BED format" />