idr: fix linter problems (#7943)

Author: bernt-matthias

tools/idr/.lint_skip

@@ -39,8 +39,8 @@
     <inputs>
         <param name="primus" argument="--samples" type="data" format="bed,gff" label="First set of peaks in GFF or BED format" />
         <param name="secundus" argument="--samples" type="data" format="bed,gff" label="Second set of peaks in GFF or BED format" />
-        <param name="peak_list" argument="--peak-list" type="data" format="bed,gff" optional="True" label="List of peaks to filter by" />
-        <param name="input_file_type" argument="--input-file-type" type="select" label="Input BED format" help="This option is ignored if the input file is GFF">
+        <param argument="--peak-list" type="data" format="bed,gff" optional="True" label="List of peaks to filter by" />
+        <param argument="--input-file-type" type="select" label="Input BED format" help="This option is ignored if the input file is GFF">
             <option value="" selected="true">Vanilla BED</option>
             <option value="gff">GFF</option>
             <option value="broadPeak">ENCODE broadPeak</option>
@@ -52,29 +52,29 @@
             <option value="p.value">p value</option>
             <option value="q.value">q value</option>
         </param>
-        <param name="idr_threshold" argument="--idr-threshold" type="float" optional="true" value="" />
-        <param name="soft_idr_threshold" argument="--soft-idr-threshold" type="float" value="0.05" />
+        <param argument="--idr-threshold" type="float" optional="true" value="" />
+        <param argument="--soft-idr-threshold" type="float" value="0.05" />
         <param argument="--plot" type="boolean" truevalue="--plot" falsevalue="" label="Output PNG plot of peaks" />
-        <param name="use_nonoverlapping_peaks" argument="--use-nonoverlapping-peaks" type="boolean" truevalue="--use-nonoverlapping-peaks" falsevalue="" label="Use peaks without an overlapping match and set the value to 0" />
-        <param name="peak_merge_method" argument="--peak-merge-method" type="select" label="Method to use for merging peaks">
+        <param argument="--use-nonoverlapping-peaks" type="boolean" truevalue="--use-nonoverlapping-peaks" falsevalue="" label="Use peaks without an overlapping match and set the value to 0" />
+        <param argument="--peak-merge-method" type="select" label="Method to use for merging peaks">
             <option value="sum">Sum</option>
             <option value="avg">Average</option>
             <option value="min">Min</option>
             <option value="max">Max</option>
         </param>
-        <param name="initial_mu" argument="--initial-mu" type="float" value="0.1" label="Initial value of mu" />
-        <param name="initial_sigma" argument="--initial-sigma" type="float" value="1.0" label="Initial value of sigma" />
-        <param name="initial_rho" argument="--initial-rho" type="float" value="0.2" label="Initial value of rho" />
-        <param name="initial_mix_param" argument="--initial-mix-param" type="float" value="0.5" label="Initial value of the mixture parameters" />
-        <param name="fix_mu" argument="--fix-mu" type="boolean" truevalue="--fix-mu" falsevalue="" label="Fix mu to the starting point and do not let it vary" />
-        <param name="fix_sigma" argument="--fix-sigma" type="boolean" truevalue="--fix-sigma" falsevalue="" label="Fix sigma to the starting point and do not let it vary" />
-        <param name="dont_filter_peaks_below_noise_mean" argument="--dont-filter-peaks-below-noise-mean" type="boolean" truevalue="--dont-filter-peaks-below-noise-mean" falsevalue="" label="Allow signal points that are below the noise mean" />
+        <param argument="--initial-mu" type="float" value="0.1" label="Initial value of mu" />
+        <param argument="--initial-sigma" type="float" value="1.0" label="Initial value of sigma" />
+        <param argument="--initial-rho" type="float" value="0.2" label="Initial value of rho" />
+        <param argument="--initial-mix-param" type="float" value="0.5" label="Initial value of the mixture parameters" />
+        <param argument="--fix-mu" type="boolean" truevalue="--fix-mu" falsevalue="" label="Fix mu to the starting point and do not let it vary" />
+        <param argument="--fix-sigma" type="boolean" truevalue="--fix-sigma" falsevalue="" label="Fix sigma to the starting point and do not let it vary" />
+        <param argument="--dont-filter-peaks-below-noise-mean" type="boolean" truevalue="--dont-filter-peaks-below-noise-mean" falsevalue="" label="Allow signal points that are below the noise mean" />
         <param name="use_best_multisummit_idr" argument="--use-best-multisummit-IDR" type="boolean" truevalue="--use-best-multisummit-IDR" falsevalue="" label="Set the IDR value for a group of multi summit peaks" help="A group of peaks with the same chr/start/stop but different summits" />
-        <param name="allow_negative_scores" argument="--allow-negative-scores" type="boolean" truevalue="--allow-negative-scores" falsevalue="" label="Allow negative values for scores" />
-        <param name="random_seed" argument="--random-seed" type="integer" value="0" label="The random seed value" />
-        <param name="max_iter" argument="--max-iter" type="integer" value="3000" label="The maximum number of optimization iterations" />
-        <param name="convergence_eps" argument="--convergence-eps" type="float" value="0.000001" label="The maximum change in parameter value changes for convergence" />
-        <param name="only_merge_peaks" argument="--only-merge-peaks" type="boolean" truevalue="--only-merge-peaks" falsevalue="" label="Only return the merged peak list" />
+        <param argument="--allow-negative-scores" type="boolean" truevalue="--allow-negative-scores" falsevalue="" label="Allow negative values for scores" />
+        <param argument="--random-seed" type="integer" value="0" label="The random seed value" />
+        <param argument="--max-iter" type="integer" value="3000" label="The maximum number of optimization iterations" />
+        <param argument="--convergence-eps" type="float" value="0.000001" label="The maximum change in parameter value changes for convergence" />
+        <param argument="--only-merge-peaks" type="boolean" truevalue="--only-merge-peaks" falsevalue="" label="Only return the merged peak list" />
     </inputs>
     <outputs>
         <data format="bed" name="idr_values" from_work_dir="idrValues.bed" label="${tool.name} on ${on_string}: IDR Values">
@@ -89,23 +89,23 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="primus" value="idr_input1.1.bed" ftype="bed" />
             <param name="secundus" value="idr_input1.2.bed" ftype="bed" />
             <param name="rank" value="default" />
             <param name="plot" value="True" />
             <output name="idr_values" file="idr_out1.bed" ftype="bed" />
             <output name="idr_plot" file="idr_out1.png" ftype="png" compare="sim_size" delta="1000"/>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="primus" value="idr_input2.1.bed" ftype="bed" />
             <param name="secundus" value="idr_input2.2.bed" ftype="bed" />
             <param name="rank" value="default" />
             <param name="plot" value="True" />
             <output name="idr_values" file="idr_out2.bed" ftype="bed" />
             <output name="idr_plot" file="idr_out2.png" ftype="png" compare="sim_size" delta="1000"/>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="primus" value="idr_input3.1.bed" ftype="bed" />
             <param name="secundus" value="idr_input3.2.bed" ftype="bed" />
             <param name="peak_list" value="idr_input3.3.bed" ftype="bed" />
@@ -114,7 +114,7 @@
             <output name="idr_values" file="idr_out3.bed" ftype="bed" />
             <output name="idr_plot" file="idr_out3.png" ftype="png" compare="sim_size" delta="1000"/>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="primus" value="idr_input4.1.gff" ftype="gff" />
             <param name="secundus" value="idr_input4.2.gff" ftype="gff" />
             <param name="input_file_type" value="gff" />