blocks|key|142473|text|rule+hello:
++++output:
++++++++"woot",+"hoot"
++++run:
++++++++for+f+in+output:
++++++++++++print(f)
++++++++print(output[1])|type|code-block|depth|inlineStyleRanges|entityRanges|data|syntax|javascript|142474|印上“呜呜”、“呜呜”、“呜呜”。|unstyled|142475|entityMap^0|0|0^^$0|@$1|2|3|4|5|6|7|I|8|@]|9|@]|A|$B|C]]|$1|D|3|E|5|F|7|J|8|@]|9|@]|A|$]]|$1|G|3|-4|5|F|7|K|8|@]|9|@]|A|$]]]|H|$]]

<pre><code>rule hello:
 output:
 "woot", "hoot"
 run:
 for f in output:
 print(f)
 print(output[1])
</code></pre>

prints "woot", "hoot", "hoot".

blocks|key|659217|text|如果我正确理解您的问题，您的问题是neo4j.py脚本不能为其-output参数接受多个文件:+shell命令可能以完整的文件列表(使用snakemake的-p选项检查)结束，但是脚本只考虑了第一个文件。|type|unstyled|depth|inlineStyleRanges|offset|length|style|CODE|entityRanges|data|659218|如果确实如此，一种可能更简洁的方法是修改neo4j.py脚本的接口，以便它为每个输出文件使用一个参数。|659219|然后，您将修改规则如下：|659220|rule+neo4j:
++++input:
++++++++script+=+'python/neo4j.py',
++++++++path_to_cl+=+'results/clusters/umap/{sample}_umap_clusters.csv',
++++++++path_to_umap+=+'results/umap/{sample}_umap.csv',
++++++++path_to_mtx+=+'data_files/normalized/{sample}.csv'
++++output:
++++++++cells+=+'results/neo4j/{sample}/cells.csv',
++++++++genes+=+'results/neo4j/{sample}/genes.csv',
++++++++nodes+=+'results/neo4j/{sample}/cl_nodes.csv',
++++++++contains+=+'results/neo4j/{sample}/cl_contains.csv',
++++++++isin+=+'results/neo4j/{sample}/cl_isin.csv',
++++++++by+=+'results/neo4j/{sample}/expr_by.csv',
++++++++ess+=+'results/neo4j/{sample}/expr_ess.csv'
++++shell:
++++++++"""
++++++++python+{input.script}+\\
++++++++++++--path_to_cl+{input.path_to_cl}+\\
++++++++++++--path_to_umap+{input.path_to_umap}+\\
++++++++++++--path_to_mtx+{input.path_to_mtx}+\\
++++++++++++--cells+{output.cells}+\\
++++++++++++--genes+{output.genes}+\\
++++++++++++--nodes+{output.nodes}+\\
++++++++++++--contains+{output.contains}+\\
++++++++++++--isin+{output.isin}+\\
++++++++++++--by+{output.by}+\\
++++++++++++--ess+{output.ess}
++++++++"""|code-block|syntax|javascript|659221|一些可能有用的python模块用于设置脚本的接口：|659222|多多普|unordered-list-item|659223|argparse解析|659224|编辑|659225|如果不希望将每个输入文件作为单独的参数传递，则只需传递输出目录，并让脚本从这个单个参数构建输出路径。给定您想要的文件名，这似乎是可能的：|659226|rule+neo4j:
++++input:
++++++++script+=+'python/neo4j.py',
++++++++path_to_cl+=+'results/clusters/umap/{sample}_umap_clusters.csv',
++++++++path_to_umap+=+'results/umap/{sample}_umap.csv',
++++++++path_to_mtx+=+'data_files/normalized/{sample}.csv'
++++output:
++++++++'results/neo4j/{sample}/cells.csv',
++++++++'results/neo4j/{sample}/genes.csv',
++++++++'results/neo4j/{sample}/cl_nodes.csv',
++++++++'results/neo4j/{sample}/cl_contains.csv',
++++++++'results/neo4j/{sample}/cl_isin.csv',
++++++++'results/neo4j/{sample}/expr_by.csv',
++++++++'results/neo4j/{sample}/expr_ess.csv'
++++shell:
++++++++"""
++++++++python+{input.script}+\\
++++++++++++--path_to_cl+{input.path_to_cl}+\\
++++++++++++--path_to_umap+{input.path_to_umap}+\\
++++++++++++--path_to_mtx+{input.path_to_mtx}+\\
++++++++++++--out_dir+results/neo4j/{wildcards.sample}
++++++++"""|659227|entityMap|0|LINK|mutability|MUTABLE|url|https://github.com/docopt/docopt|1|https://docs.python.org/3/howto/argparse.html^0|H|8|V|7|1W|9|26|2|0|K|8|0|0|0|0|0|3|0|0|0|A|1|0|0|0|0^^$0|@$1|2|3|4|5|6|7|1B|8|@$9|1C|A|1D|B|C]|$9|1E|A|1F|B|C]|$9|1G|A|1H|B|C]|$9|1I|A|1J|B|C]]|D|@]|E|$]]|$1|F|3|G|5|6|7|1K|8|@$9|1L|A|1M|B|C]]|D|@]|E|$]]|$1|H|3|I|5|6|7|1N|8|@]|D|@]|E|$]]|$1|J|3|K|5|L|7|1O|8|@]|D|@]|E|$M|N]]|$1|O|3|P|5|6|7|1P|8|@]|D|@]|E|$]]|$1|Q|3|R|5|S|7|1Q|8|@]|D|@$9|1R|A|1S|1|1T]]|E|$]]|$1|T|3|U|5|S|7|1U|8|@]|D|@$9|1V|A|1W|1|1X]]|E|$]]|$1|V|3|W|5|6|7|1Y|8|@]|D|@]|E|$]]|$1|X|3|Y|5|6|7|1Z|8|@]|D|@]|E|$]]|$1|Z|3|10|5|L|7|20|8|@]|D|@]|E|$M|N]]|$1|11|3|-4|5|6|7|21|8|@]|D|@]|E|$]]]|12|$13|$5|14|15|16|E|$17|18]]|19|$5|14|15|16|E|$17|1A]]]]

If I understand correctly your issue, your problem is that the <code>neo4j.py</code> script doesn't accept more than one file for its <code>-output</code> argument: The shell command probably ends with the full list of files (check with the <code>-p</code> option of <code>snakemake</code>), but only the first one is taken into account by the script.

If that is indeed the case, a possibly cleaner approach would be to modify the interface of your <code>neo4j.py</code> script so that it uses one argument for each of its output files.

You would then modify your rule as follows:

<pre><code>rule neo4j:
 input:
 script = 'python/neo4j.py',
 path_to_cl = 'results/clusters/umap/{sample}_umap_clusters.csv',
 path_to_umap = 'results/umap/{sample}_umap.csv',
 path_to_mtx = 'data_files/normalized/{sample}.csv'
 output:
 cells = 'results/neo4j/{sample}/cells.csv',
 genes = 'results/neo4j/{sample}/genes.csv',
 nodes = 'results/neo4j/{sample}/cl_nodes.csv',
 contains = 'results/neo4j/{sample}/cl_contains.csv',
 isin = 'results/neo4j/{sample}/cl_isin.csv',
 by = 'results/neo4j/{sample}/expr_by.csv',
 ess = 'results/neo4j/{sample}/expr_ess.csv'
 shell:
 """
 python {input.script} \\
 --path_to_cl {input.path_to_cl} \\
 --path_to_umap {input.path_to_umap} \\
 --path_to_mtx {input.path_to_mtx} \\
 --cells {output.cells} \\
 --genes {output.genes} \\
 --nodes {output.nodes} \\
 --contains {output.contains} \\
 --isin {output.isin} \\
 --by {output.by} \\
 --ess {output.ess}
 """
</code></pre>

Some potentially useful python modules to set up the interface of your script:

<ul>
<li><a href="https://github.com/docopt/docopt" rel="nofollow noreferrer">docopt</a></li>
<li><a href="https://docs.python.org/3/howto/argparse.html" rel="nofollow noreferrer">argparse</a></li>
</ul>

<hr>

<h3>Edit</h3>

If you don't want to pass each input file as an individual argument, you could simply pass the output directory, and let your script build the output paths from this single parameters. Given the file names you want, this seems possible:

<pre><code>rule neo4j:
 input:
 script = 'python/neo4j.py',
 path_to_cl = 'results/clusters/umap/{sample}_umap_clusters.csv',
 path_to_umap = 'results/umap/{sample}_umap.csv',
 path_to_mtx = 'data_files/normalized/{sample}.csv'
 output:
 'results/neo4j/{sample}/cells.csv',
 'results/neo4j/{sample}/genes.csv',
 'results/neo4j/{sample}/cl_nodes.csv',
 'results/neo4j/{sample}/cl_contains.csv',
 'results/neo4j/{sample}/cl_isin.csv',
 'results/neo4j/{sample}/expr_by.csv',
 'results/neo4j/{sample}/expr_ess.csv'
 shell:
 """
 python {input.script} \\
 --path_to_cl {input.path_to_cl} \\
 --path_to_umap {input.path_to_umap} \\
 --path_to_mtx {input.path_to_mtx} \\
 --out_dir results/neo4j/{wildcards.sample}
 """
</code></pre>

I am trying to feed all of the paths at once in one variable to a <code>python</code> script in <code>snakemake</code> like that: 

<pre><code>rule neo4j:
 input:
 script = 'python/neo4j.py',
 path_to_cl = 'results/clusters/umap/{sample}_umap_clusters.csv',
 path_to_umap = 'results/umap/{sample}_umap.csv',
 path_to_mtx = 'data_files/normalized/{sample}.csv'
 output: 'results/neo4j/{sample}/cells.csv', 'results/neo4j/{sample}/genes.csv', 
 'results/neo4j/{sample}/cl_nodes.csv', 'results/neo4j/{sample}/cl_contains.csv',
 'results/neo4j/{sample}/cl_isin.csv', 'results/neo4j/{sample}/expr_by.csv',
 'results/neo4j/{sample}/expr_ess.csv'
 shell:
 "python {input.script} -path_to_cl {input.path_to_cl} -path_to_umap {input.path_to_umap} -path_to_mtx {input.path_to_mtx} -output {output}"
</code></pre>

When I am accessing <code>output</code> parameter in the <code>python</code> script it sees only the first path: <code>'results/neo4j/{sample}/cells.csv'</code>. I have also tried naming each path, but it did not fix the issue. How to pass all paths in the <code>output</code> of the rule as an array or as dictionary to be able to access them later in <code>python</code>?

Snakemake passes only the first path in the output to shell command

翻译质量差，导致语言生硬或混乱。

没有提供实际的解决方法或示例。

解答不清晰，无法理解或解决问题。

页面排版不美观，阅读体验差。

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我试图将一个变量中的所有路径同时提供给snakemake中的一个snakemake脚本，如下所示：rule neo4j:  input:      script = 'python/neo4j.py',      path_to_cl = 'results/clusters/umap/{sample}_umap_clu...

问Snakemake只将输出中的第一个路径传递给shell命令。
EN

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问Snakemake只将输出中的第一个路径传递给shell命令。EN