Galaxy |

Changeset 1:ca22d8497db5 (2020-01-19)

Previous changeset 0:64a83664b814 (2017-12-19) Next changeset 2:c5c5a3e84989 (2024-09-27)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"

modified:
macros.xml
poretools_yield_plot.xml

removed:
test-data/poretools-events-out1.tabular
test-data/poretools-events-out2.tabular

diff -r 64a83664b814 -r ca22d8497db5 macros.xml
--- a/macros.xml Tue Dec 19 14:54:20 2017 -0500
+++ b/macros.xml Sun Jan 19 09:10:18 2020 -0500

[

@@ -47,4 +47,6 @@
         <param name="min_length" argument="--min-length" type="integer" value="0" label="Minimum read length" />
         <param name="max_length" argument="--max-length" type="integer" value="1000000000" label="Maximum read length" />
     </xml>
+    <token name="@MPLBACKEND@"><![CDATA[export MPLBACKEND="agg" &&]]></token>
+    <token name="@profile@">18.09</token>
</macros>

diff -r 64a83664b814 -r ca22d8497db5 poretools_yield_plot.xml
--- a/poretools_yield_plot.xml Tue Dec 19 14:54:20 2017 -0500
+++ b/poretools_yield_plot.xml Sun Jan 19 09:10:18 2020 -0500

[

@@ -1,18 +1,19 @@
<?xml version="1.0"?>
-<tool id="poretools_yield_plot" name="Collector’s curve" version="@VERSION@.0">
+<tool id="poretools_yield_plot" name="Collector’s curve" version="@VERSION@.1">
     <description>of sequencing yield over time</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="requirements"/>
     <command detect_errors="aggressive">
     <![CDATA[
-        poretools yield_plot '$input' --saveas plot.$extension --plot-type $plot_type
-            $theme_bw
-        #if $skip != '0':
-            --skip $skip
-        #end if
-        && mv plot.$extension '$output'
+@MPLBACKEND@
+poretools yield_plot '$input' --saveas plot.$extension --plot-type $plot_type
+    $theme_bw
+#if $skip != '0':
+    --skip $skip
+#end if
+&& mv plot.$extension '$output'
     ]]>
     </command>
     <inputs>
@@ -21,7 +22,7 @@
             <option value="reads">Reads</option>
             <option value="basepairs">Base pairs</option>
         </param>
-        <param argument="--skip" type="integer" value="0" label="Plot only every nth point" help="Increases performance at the cost of resolution." />
+        <param argument="--skip" type="integer" min="1" value="1" label="Plot only every nth point" help="Increases performance at the cost of resolution." />
         <expand macro="plot_options" />
     </inputs>
     <outputs>
@@ -32,13 +33,13 @@
             <expand macro="test_input" />
             <param name="extension" value="png" />
             <param name="plot_type" value="reads" />
-            <output name="output" file="poretools-yield-plot-out1.png" ftype="png" lines_diff="301" />
+            <output name="output" file="poretools-yield-plot-out1.png" ftype="png" compare="sim_size" />
         </test>
         <test>
             <expand macro="test_input" />
             <param name="extension" value="svg" />
             <param name="plot_type" value="basepairs" />
-            <output name="output" file="poretools-yield-plot-out2.svg" ftype="svg" lines_diff="40" />
+            <output name="output" file="poretools-yield-plot-out2.svg" ftype="svg" lines_diff="50" />
         </test>
     </tests>
     <help>

diff -r 64a83664b814 -r ca22d8497db5 test-data/poretools-events-out1.tabular
--- a/test-data/poretools-events-out1.tabular Tue Dec 19 14:54:20 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,3083 +0,0 @@\n-file\tstrand\tmean\tstart\tstdv\tlength\tmodel_state\tmodel_level\tmove\tp_model_state\tmp_model_state\tp_mp_model_state\tp_A\tp_C\tp_G\tp_T\traw_index\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t52.3276716165\t955054\t5.19878084063\t17\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t45.2667833984\t955071\t1.3678974514\t25\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t55.5428768382\t955096\t4.1309184471\t17\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t81.4959472656\t955113\t5.98801696437\t14\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t89.1865418294\t955127\t0.657985513478\t15\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t91.2216268884\t955142\t0.745442845871\t83\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t96.1968325806\t955225\t1.15534444131\t16\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t103.919551047\t955241\t0.794076774485\t46\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t101.314279896\t955287\t0.822017489553\t44\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t100.386008718\t955331\t0.742245579983\t41\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t95.4147277114\t955372\t3.92378517962\t17\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t63.8099826979\t955389\t2.86295254004\t46\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t47.135785945\t955435\t3.62179282491\t13\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t49.9494964765\t955448\t0.880898121478\t74\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t45.6114414535\t955522\t0.847339570401\t31\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t48.8273132324\t955553\t1.15910314268\t10\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t58.1400206163\t955563\t1.22364592088\t18\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t55.4368709697\t955581\t0.693719620924\t63\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t48.6955848694\t955644\t0.735672299594\t48\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t46.670480835\t955692\t0.930210779204\t20\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t50.8330971069\t955712\t0.599838504324\t40\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t51.5953652344\t955752\t0.528736930214\t20\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t50.9771201172\t955772\t0.515119099554\t25\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t57.2696376546\t955797\t1.42077376312\t12\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t55.2506391253\t955809\t0.816167400725\t14\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t51.5120627267\t955823\t0.899186651723\t28\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t54.424305013\t955851\t0.878111022192\t12\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t61.5552003988\t955863\t1.30487853179\t12\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5\tpre_basecalled\t57.5551616962\t955875\t0.852089537407\t26\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3'..b'\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t61.6277973633\t7453325\t2.88453554658\t10\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t44.9266264012\t7453335\t0.819536262462\t23\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t60.9070624138\t7453358\t2.41436171329\t34\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t66.4789138794\t7453392\t1.66021873338\t24\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t59.4294505726\t7453416\t0.812132551954\t22\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t62.4659715735\t7453438\t1.5416234218\t46\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t69.231409389\t7453484\t0.75653773971\t28\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t67.417189588\t7453512\t0.939540341216\t76\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t47.6601716072\t7453588\t3.37496820371\t31\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t50.1493869851\t7453619\t2.00012829539\t11\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t62.049328125\t7453630\t1.69686130579\t10\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t67.7058694894\t7453640\t1.45234007624\t14\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t62.5329175822\t7453654\t1.32462694054\t24\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t54.4883974095\t7453678\t0.699704157439\t76\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t61.1651943735\t7453754\t1.30813881409\t13\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t57.8768426804\t7453767\t1.472346694\t21\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t56.653734375\t7453788\t0.7535333175\t10\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t58.6161942546\t7453798\t0.486178112543\t12\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t67.2674352385\t7453810\t0.970106950782\t19\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t60.4629475682\t7453829\t1.43149065719\t71\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t72.9248217773\t7453900\t1.64248527867\t28\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t64.8744107594\t7453928\t2.21840032736\t17\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t68.8500244141\t7453945\t0.659051509339\t10\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t65.2529619141\t7453955\t0.864337951367\t10\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t70.3429458618\t7453965\t1.92585885653\t16\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t64.2192951766\t7453981\t0.753235095042\t23\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t66.4051459961\t7454004\t1.11915336722\t10\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t61.5801460598\t7454014\t0.692357388262\t23\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t52.8637896174\t7454037\t1.38964558335\t44\t\t\t\t\t\t\t\t\t\t\n-.poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5\tpre_basecalled\t43.7066423754\t7454081\t1.37303297158\t53\t\t\t\t\t\t\t\t\t\t\n'

diff -r 64a83664b814 -r ca22d8497db5 test-data/poretools-events-out2.tabular
--- a/test-data/poretools-events-out2.tabular Tue Dec 19 14:54:20 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000